<PAGE>   1
                                                                     EXHIBIT 9.4

                        THIRD AMENDMENT TO FIRST AMENDED
                        AND RESTATED INVESTORS' AGREEMENT


       This Third Amendment to the First Amended and Restated Investors'
Agreement (this "Agreement") dated as of April 8, 1999, is entered into by and
among (i) Doane Pet Care Enterprises, Inc., formerly known as DPC Acquisition
Corp. (the "Company"), (ii) Doane Pet Care Company formerly known as Doane
Products Company ("Doane"), (iii) Summit Capital Inc. ("Summit"), (iv)
Summit/DPC Partners, L.P. ("Summit/DPC"), (v) Chase Manhattan Investment
Holdings, Inc. ("Chase"), (vi) DLJ Merchant Banking Partners, L.P., DLJ
International Partners, C.V., DLJ Offshore Partners, C.V., DLJ Merchant Banking
Funding, Inc., DLJ First ESC, L.L.C., (each of the foregoing in this clause
(vi), a "DLJ Entity," and collectively, the "DLJ Entities"), (vii) Dartford
Partnership, L.L.C. ("Dartford"), (viii) Bruckmann, Rosser, Sherrill & Co., L.P.
("BRS"), (ix) PNC Capital Corp ("PNC"), (x) Windy Hill Pet Food Company, L.L.C.
("Windy Hill L.L.C."), (xi) Baseball Partners and (xii) the other Persons listed
on the signature pages hereto.

                              W I T N E S S E T H :

       WHEREAS, certain stockholders and warrantholders of the Company are
parties to or bound by that certain First Amended and Restated Investors'
Agreement dated as of August 3, 1998, as amended to date (the "Original
Agreement");

       WHEREAS, the parties hereto wish to reflect that the DLJ Entities will no
longer be a party to the governance provisions contained herein but will remain
subject to the provisions in Article 5 and Article 7; and

       WHEREAS, the undersigned, constituting the holders of more than 75% of
the shares of Common Stock of the Company (including the Warrants on an "as-if
exercised" basis) desire to amend the Original Agreement on the terms of this
Agreement and, except as amended by this Agreement, ratify the terms of the
Original Agreement.

       NOW, THEREFORE, for good and valuable consideration, the receipt and
sufficiency of which are hereby acknowledged, and in exchange for the mutual
covenants herein, the parties hereto agree as follows:

                                   AGREEMENTS

1.     Defined Terms. Capitalized terms used in this Agreement that are not
defined herein shall have the meanings given to them in the Original Agreement.

2.     Amendments. From and after the IPO Closing Date (as defined below), the
Original Agreement shall be amended as follows:


<PAGE>   2



       (a)    Section 1.1(a) is amended by adding the following defined terms:

                    "BYLAWS" means the bylaws of the Company, as amended or 
              restated from time to time.

                    "CLASS I DIRECTOR" means any director of the Board then 
              serving in one of the Board positions specified as a "Class I"
              position by the Bylaws of Company.

                    "CLASS II DIRECTOR" means any director of the Board then
              serving in one of the Board positions specified as a "Class II"
              position by the Bylaws of Company.

                    "CLASS III DIRECTOR" means any director of the Board then
              serving in one of the Board positions specified as a "Class III"
              position by the Bylaws of Company.

                    "IPO CLOSING DATE" means the date on which an Initial Public
              Offering is consummated.

                    "SHAREHOLDER" means each Person (other than the Company or
              Doane) who shall be a party to this Agreement, whether in
              connection with the execution and delivery hereof as of the date
              hereof, pursuant to Section 7.3 or otherwise, or bound by this
              Agreement by reason of being a party to the Original Agreement, in
              each case, so long as such Person shall beneficially own any
              Securities; provided, however, that the term "Shareholder" shall
              not include and shall not create benefits or obligations with
              respect to any of the DLJ Entities other than such benefits and
              obligations provided in Article 5 and Article 7.

       (b)    Section 2.1(a) is hereby amended in its entirety to provide as
              follows:

              "(a)  From and after the IPO Closing Date, the Board shall consist
              of eight members or such greater number as is established in
              accordance with the Bylaws, and the Company shall take such action
              as is necessary to cause the following persons to be nominated, in
              accordance with the Bylaws, to stand for election to serve as
              directors in the positions (i.e., as Class I Directors, Class II
              Directors or Class III Directors) specified below:

                    (i)   (A) at any time the Summit-Investors own of record 50%
                    or more of the number of shares of Common Stock owned
                    thereby as of August 3, 1998 (in each case, disregarding
                    stock splits, recapitalizations and similar adjustments in
                    number of shares and stock dividends), two individuals
                    designated by Summit on behalf of the Summit-Investors, and,
                    as long as the Board is classified, of such two individuals,
                    one shall stand for election as a Class III Director and the
                    second individual shall stand for election as a

                                      -2-
<PAGE>   3
                    Class II Director (each such person, a "SUMMIT-INVESTOR
                    DESIGNEE") and (B) at any time the Summit-Investors own of
                    record less than 50% of the number of shares of Common Stock
                    owned thereby as of August 3, 1998 (disregarding stock
                    splits, recapitalizations, and similar adjustments in
                    number of shares and stock dividends) and the
                    Summit-Investors' Percentage Ownership is 5% or more, one
                    individual designated by Summit on behalf of the
                    Summit-Investors and, so long as the Board is classified,
                    such individual shall stand for election as a Class III
                    Director;

                    (ii)   (A) at any time the Windy Hill Investors own of 
                    record (or beneficially by reason of the record ownership of
                    IBJ Whitehall Bank & Trust Company (formerly IBJ Schroder
                    Bank & Trust Company) ("IBJ")) 50% or more of the number of
                    shares of Common Stock owned thereby as of August 3, 1998
                    (in each case, disregarding stock splits, recapitalizations
                    and similar adjustments in number of shares and stock
                    dividends), one individual designated by Windy Hill L.L.C.,
                    which individual shall stand for election as a Class II
                    Director, and one individual designated by BRS, which
                    individual shall stand for election as a Class I Director
                    (such two designees collectively referred to as the "Windy
                    Hill Designees" or individually as a "Windy Hill Designee")
                    and (B) at any time the Windy Hill Investors own of record
                    (or beneficially by reason of the record ownership of IBJ
                    less than 50% of the number of shares of Common Stock owned
                    thereby as of August 3, 1998 (in each case, disregarding
                    stock splits, recapitalizations and similar adjustments in
                    number of shares and stock dividends) and the Windy Hill
                    Investors' Percentage Ownership is 5% or more, the Windy
                    Hill Representative (which, the Windy Hill Investors hereby
                    agree, shall initially be Ray Chung) shall be nominated to
                    stand for election and, so long as the Board is classified,
                    the Windy Hill Representative shall stand for election to
                    serve as a Class II Director;

                    (iii)   at any time the Chase Percentage Ownership is 5% or
                    greater, one individual shall be designated by Chase (the
                    "CHASE DESIGNEE") to stand for election and, so long as the
                    Board is classified, the Chase Designee shall stand for
                    election to serve as a Class III Director;

                    (iv)   the chief executive officer of the Company shall be
                    designated to stand for election and, so long as the Board
                    is classified, the chief executive officer shall stand for
                    election to serve as a Class II Director; and

                    (v)   in addition to the individuals contemplated above, at
                    any time the Summit-Investors' Percentage Ownership is 5% or
                    more, one individual designated by George B. Kelly (so long
                    as Mr. Kelly serves as a member of the Board) or, if Mr.
                    Kelly is not then serving on the Board, designated by the
                    Summit-Investor Designee or Designees then serving on the
                    Board, to stand for election to serve as a Class II Director
                    (the "Kelly Designee").


                                      -3-
<PAGE>   4

                    Director positions for which a nominee is not specified in
              accordance with the preceding provisions of this Section 2.2(a)
              shall be specified in accordance with the Bylaws; provided, the
              initial nominees for such positions shall be nominated by a
              majority of the other individuals nominated or designated in
              accordance with the preceding provisions of this Section 2.2(a),
              or in the absence of such majority, by the Chairman of the Board.

                    At the Company's request, each Shareholder entitled to vote
              for the election of directors to the Board shall vote its
              Securities and execute written consents to increase the Board size
              and to elect independent directors to accommodate the requirements
              for listing the Securities on any national securities exchange or
              market system on which the Board determines that the Securities
              shall be listed or included or to include at least two individuals
              who are "Non-Employee Directors" for purposes of, and as such term
              is referred to in, Rule 16b-3 of the Exchange Act. Each
              Shareholder entitled to vote for the election of directors to the
              Board agrees that it will vote its Securities or execute consents,
              as the case may be, and take all other reasonable action
              (including taking reasonable steps to cause the Company to call a
              special meeting of shareholders) in order to ensure that the
              composition of the Board is as set forth in this Section 2.1(a).
              The parties to this Agreement acknowledge and agree that, due to
              the existence of stockholders entitled to vote for the election of
              directors that are not parties to this Agreement, the right to
              designate an individual pursuant to this Section 2.1(a) and the
              obligations of the Shareholders to vote for or consent to any
              individual designated in accordance with this Section 2.1(a) may
              not be sufficient to ensure that such individual shall be elected
              to the Board."

       (c)    Section 2.2 is hereby amended in its entirety to provide as
              follows:

              "Removal and Resignation.

                    (a)   Each Shareholder agrees that it will not vote any of 
                    its Securities in favor of the removal of any director who
                    shall have been designated or nominated pursuant to Section
                    2.1(a) unless (i) such removal shall be for Cause (as
                    defined below) or (ii) the Person(s) entitled to designate
                    or nominate such director shall have consented to or
                    requested such removal in writing (and, in the case of any
                    such request, such Shareholder shall vote its Securities in
                    favor of such removal). Removal for "Cause" shall mean
                    removal of a director because of such director's (A) willful
                    and continued failure substantially to perform his duties
                    with the Company in his established position, (B) willful
                    conduct which is injurious to the Company or any of its
                    Subsidiaries, monetarily or otherwise, (C) conviction for,
                    or guilty plea to, a felony or a crime involving moral
                    turpitude, (D) abuse of illegal drugs or other controlled
                    substances or habitual intoxication or (E) willful breach of
                    this Agreement.

                    (b)   (i) At any time there are two Summit-Investor 
                    Designees serving on the Board when (A) the Summit-Investors
                    own of record less than 50% of the


                                       -4-
<PAGE>   5
                    number of shares of Common Stock owned thereby as of August
                    3, 1999 (disregarding stock splits, recapitalizations and
                    similar adjustments in the number of shares and stock
                    dividends) and (B) the Summit-Investors' Percentage
                    Ownership is 5% or greater, upon the request of a majority
                    of the other directors, the Summit-Investors shall use their
                    commercial best efforts to cause one of the two
                    Summit-Investor Designees to resign, and the resigning
                    Summit-Investor Designee shall be the individual identified
                    by George B. Kelly or, if Mr. Kelly fails to identify the
                    resigning Summit-Investor Designee, the resigning
                    Summit-Investor Designee shall be the Summit-Investor
                    Designee that is not Mr. Kelly or (ii) at any time there are
                    any Summit-Investor Designees serving on the Board when the
                    Summit-Investors' Percentage Ownership is less than 5%, upon
                    the request of a majority of the other directors of the
                    Board, the Summit-Investors shall use their commercial best
                    efforts to cause each Summit-Investor Designee and the Kelly
                    Designee to resign from the Board;

                    (c)   (i) At any time there are two Windy Hill Designees
                    serving on the Board when (A) the Windy Hill Investors own
                    of record (or beneficially by reason of the record ownership
                    of IBJ) less than 50% of the number of shares of Common
                    Stock owned thereby as of August 3, 1999 (disregarding stock
                    splits, recapitalizations and similar adjustments in the
                    number of shares and stock dividends) and (B) the Windy Hill
                    Investors' Percentage Ownership is 5% or greater, upon the
                    request of a majority of the other directors, the Windy Hill
                    Investors shall use their commercial best efforts to cause
                    one of the two Windy Hill Investor Designees to resign, and
                    the resigning Windy Hill Designee shall be the individual
                    identified by the Windy Hill Representative or, if the Windy
                    Hill Representative fails to identify the resigning Windy
                    Hill Designee, the resigning Windy Hill Designee shall be
                    the Windy Hill Designee that is not the Windy Hill
                    Representative or (ii) at any time there are any Windy Hill
                    Designees serving on the Board when the Windy Hill
                    Investors' Percentage Ownership is less than 5%, upon the
                    request of a majority of the other directors of the Board,
                    the Windy Hill Investors shall use their commercial best
                    efforts to cause each Windy Hill Designee to resign from the
                    Board;

                    (d)   at any time the Chase Designee is serving on the
                    Board when Chase's Percentage Ownership is less than 5%,
                    upon the request of a majority of the other directors of the
                    Board, Chase shall use its commercial best efforts to cause
                    the Chase Designee to resign from the Board;

       (d)    Section 2.3 is hereby amended in its entirety to provide as
              follows:

              2.3   Vacancies. The Shareholders recognize that under the terms
              of the certificate of incorporation and the bylaws that any
              vacancy in the Board, whether arising through death, resignation,
              or removal of a director, or through an increase in the number of
              directors of any class, shall be filled by the majority vote of
              the remaining


                                      -5-


<PAGE>   6

              directors, although less than a quorum, or by a sole remaining
              director. In the event of such vacancy, each Shareholder entitled
              to vote for the election of directors to the Board agrees that it
              will use commercial best efforts to cause its Board nominee, if
              any and if then serving on the Board, to fill any such vacancy in
              the following manner:

                    (a)   any vacancy created by the death, disability, 
                    retirement, resignation or removal of any individual (a
                    "Former Director") designated under clauses (i), (ii), (iii)
                    or (v) of Section 2.1(a) shall be filled by the applicable
                    person or persons that designated the Former Director so
                    long such person or persons remains entitled to designate an
                    individual under the applicable clause of Section 2.1(a);
                    and

                    (b)   any vacancy created by an increase in the number of
                    directors of any class shall be filled in accordance with
                    the Bylaws."

       (e)    A new Section 7.12 is hereby added to the Original Agreement and
              shall provides in its entirety as follows:

              "7.12 Termination of Certain Rights and Obligations. 
              Notwithstanding anything to the contrary in the Original
              Agreement, as amended, none of the DLJ Entities shall have any
              rights or obligations, and will not be considered a "Shareholder"
              under this Agreement other than with respect to (a) obligations or
              liabilities arising from a breach, if any, of any DLJ Entity that
              occurred prior to the IPO Closing Date, (b) rights and obligations
              under Article 5 to the extent relating to registration rights and
              (c) rights and obligations under Article 7."

3.     Terminology. The phrases "as of the date of this Agreement" and "the date
hereof," when used in the text of the Original Agreement, refer to August 3,
1998.

4.     Ratification. Except as expressly set forth herein, the terms and
provisions of the Original Agreement, as amended prior to the date hereof, are
hereby ratified and confirmed.

5.     Miscellaneous. This Agreement may be executed in one or more
counterparts, each of which shall be deemed to be an original, but all of which
shall constitute one and the same agreement.

       IN WITNESS WHEREOF, the parties hereto have caused this Agreement to be
duly executed by their respective authorized officers as of the day and year
first above written.


                                      -6-
<PAGE>   7

                                       DOANE PET CARE ENTERPRISES, INC.

                                            By: /s/ THOMAS R. HEIDENTHAL      
                                               ---------------------------------
                                            Name:   Thomas R. Heidenthal
                                                 -------------------------------
                                            Title:  Senior V.P. & C.F.O.
                                                  ------------------------------

                                       DOANE PET CARE COMPANY

                                            By: /s/ THOMAS R. HEIDENTHAL      
                                               ---------------------------------
                                            Name:   Thomas R. Heidenthal
                                                 -------------------------------
                                            Title:  Senior V.P. & C.F.O.
                                                  ------------------------------

                                       SUMMIT CAPITAL INC.

                                            By:      
                                               ---------------------------------
                                            Name:
                                                 -------------------------------
                                            Title:
                                                  ------------------------------

                                       CHASE MANHATTAN INVESTMENT
                                            HOLDINGS, INC.

                                            By: /s/ JEFFREY C. WALKER     
                                               ---------------------------------
                                            Name:   Jeffrey C. Walker
                                                 -------------------------------
                                            Title:  CEO
                                                  ------------------------------

                                       BASEBALL PARTNERS

                                            By:      
                                               ---------------------------------
                                            Name:
                                                 -------------------------------
                                            Title:
                                                  ------------------------------

                                       SUMMIT/DPC PARTNERS, L.P.

                                            BY: SUMMIT CAPITAL, INC.,
                                                    its General Partner

                                            By:      
                                               ---------------------------------
                                               Name:  George B. Kelly
                                               Title:   Chairman


                                      -7-

<PAGE>   8

                                       DLJ MERCHANT BANKING PARTNERS, L.P.,
                                            a Delaware Limited Partnership

                                            BY DLJ MERCHANT BANKING, INC.
                                                   Managing General Partner

                                            By: /s/ PETER GRAUER       
                                               ---------------------------------
                                            Name:   Peter Grauer
                                                 -------------------------------
                                            Title:  Managing Director
                                                  ------------------------------

                                       DLJ INTERNATIONAL PARTNERS, C.V.

                                            BY:  DLJ MERCHANT BANKING, INC.
                                                   Advisory General Partner

                                                   By: /s/ PETER GRAUER       
                                                      --------------------------
                                                   Name:   Peter Grauer
                                                        ------------------------
                                                   Title:  Managing Director
                                                         -----------------------

                                       DLJ OFFSHORE PARTNERS, C.V.

                                            BY: DLJ MERCHANT BANKING, INC.
                                                   Advisory General Partner

                                                   By: /s/ PETER GRAUER       
                                                      --------------------------
                                                   Name:   Peter Grauer
                                                        ------------------------
                                                   Title:  Managing Director
                                                         -----------------------

                                       DLJ FIRST ESC, L.L.C.

                                            By: /s/ PETER GRAUER       
                                               ---------------------------------
                                            Name:   Peter Grauer
                                                 -------------------------------
                                            Title:  Managing Director
                                                  ------------------------------

                                       DLJ MERCHANT BANKING FUNDING, INC.

                                            By: /s/ PETER GRAUER       
                                               ---------------------------------
                                            Name:   Peter Grauer
                                                 -------------------------------
                                            Title:  Managing Director
                                                  ------------------------------

                                       THE ROSENTHAL 1989 TRUST

                                            By:      
                                               ---------------------------------
                                            Name:
                                                 -------------------------------
                                            Title:
                                                  ------------------------------

                                      -8-

<PAGE>   9

                                      By: /s/ DICK H. WEBER
                                         ---------------------------------------
                                                    Dick H. Weber


                                      By: /s/ TERRY W. BECHTEL
                                         ---------------------------------------
                                                    Terry W. Bechtel


                                      By: 
                                         ---------------------------------------
                                                     Bob L. Robinson

                                      ROBINSON MANAGEMENT L.P.

                                            By:      
                                               ---------------------------------
                                            Name:
                                                 -------------------------------
                                            Title:
                                                  ------------------------------


                                       BOB L. ROBINSON GRANTOR RETAINED
                                       ANNUITY TRUST

                                            By:      
                                               ---------------------------------
                                            Name:
                                                 -------------------------------
                                            Title:
                                                  ------------------------------


                                       JEANINE L. ROBINSON GRANTOR RETAINED
                                       ANNUITY TRUST

                                            By:      
                                               ---------------------------------
                                            Name:
                                                 -------------------------------
                                            Title:
                                                  ------------------------------



                                      By: 
                                         ---------------------------------------
                                                    Roy E. Hess


                                      By: 
                                         ---------------------------------------
                                                    Earl R. Clements

                                      -9-

<PAGE>   10

                                      By: 
                                         ---------------------------------------
                                                    J. David Heaney


                                      By: /s/ LAURA HAWKINS MANSUR
                                         ---------------------------------------
                                                    Laura Hawkins Mansur



                                      By: /s/ WALID MANSUR
                                         ---------------------------------------
                                                     Walid Mansur


                                      THE KAREEM ROBERT MANSUR TRUST


                                      By: /s/ WALID MANSUR, TRUSTEE
                                         ---------------------------------------
                                                     Walid Mansur, Trustee


                                      THE SARA SELMA MANSUR TRUST


                                      By: /s/ WALID MANSUR, TRUSTEE
                                         ---------------------------------------
                                                     Walid Mansur, Trustee


                                      THE LEILA MARIAM MANSUR TRUST


                                      By: /s/ WALID MANSUR, TRUSTEE
                                         ---------------------------------------
                                                     Walid Mansur, Trustee



                                      By: 
                                         ---------------------------------------
                                                     Gary L. Rosenthal



                                      By: 
                                         ---------------------------------------
                                                     Lee H. Rosenthal


                                      By: 
                                         ---------------------------------------
                                                     Ferd A. Rosenthal



                                      -10-


<PAGE>   11

       The following signatories are the "Windy Hill Investors." Each of the
Windy Hill Investors and IBJ are parties to an escrow and pledge agreement dated
August 3, 1998 pursuant to which IBJ, as escrow and collateral agent, is the
record holder of all shares of Common Stock beneficially owned by the Windy Hill
Investors. Each of the undersigned Windy Hill Investors, as evidenced by its
signature below, hereby directs IBJ to enter into this Agreement.


                                     DARTFORD PARTNERSHIP, L.L.C.

                                            By: /s/ RAY CHUNG         
                                               ---------------------------------
                                            Name:   Ray Chung
                                                 -------------------------------
                                            Title:  Executive Vice President
                                                  ------------------------------


                                     BRUCKMANN, ROSSER, SHERRILL & CO., L.P.

                                            By: /s/ STEPHEN C. SHERRILL     
                                               ---------------------------------
                                            Name:   Stephen C. Sherrill
                                                 -------------------------------
                                            Title:  Managing Director
                                                  ------------------------------


                                     PNC CAPITAL CORP

                                            By:      
                                               ---------------------------------
                                            Name:
                                                 -------------------------------
                                            Title:
                                                  ------------------------------


                                     WINDY HILL PET FOOD COMPANY L.L.C.

                                            By: /s/ RAY CHUNG         
                                               ---------------------------------
                                            Name:   Ray Chung
                                                 -------------------------------
                                            Title:  Executive Vice President
                                                  ------------------------------



                                            ------------------------------------
                                                     Robert V. Dale



                                            ------------------------------------
                                                     F. Donald Cowan, Jr.


                                      -11-

<PAGE>   12


                                            ------------------------------------
                                                     Donald L. Gadd


                                            ------------------------------------
                                                     Henry G. Hurd, Jr.


                                            ------------------------------------
                                                     Ben W. McCrory


                                            ------------------------------------
                                                     Vaughn R. Oakley



                                            ------------------------------------
                                                     Charles Dunleavy


                                      -12-


<PAGE>   13


                                        BCB PARTNERSHIP, BRUCE C. BRUCKMANN,
                                        DONALD J. BRUCKMANN, PAUL D. KAMINSKI, 
                                        NAZ PARTNERSHIP, HAROLD O. ROSSER, H.
                                        VIRGIL SHERRILL, STEPHEN C. SHERRILL,
                                        NANCY A. ZWENG, ELIZABETH MCSHANE,
                                        BEVERLY PLACE, BY THE FOLLOWING
                                        PERSONS:


                                        By: /s/ STEPHEN C. SHERRILL
                                           -------------------------------------
                                           Stephen C. Sherrill, Attorney-in-Fact


                                        By: /s/ STEPHEN C. SHERRILL
                                           ------------------------------------
                                           Stephen C. Sherrill, Individually



                                        IBJ WHITEHALL BANK & TRUST COMPANY,
                                        as escrow and collateral agent and 
                                        record holder for the shares of Common
                                        Stock beneficially owned by the Windy
                                        Hill Investors set forth above.


                                        By:
                                           -------------------------------------
                                        Name: 
                                             -----------------------------------
                                        Title: 
                                              ----------------------------------


                                      -13-