<PAGE>

                                                                     Exhibit 3.1

            THIRD AMENDED AND RESTATED CERTIFICATE OF INCORPORATION
                                      OF
                          divine interVentures, inc.
                          --------------------------

          Original Certificate of Incorporation filed on May 7, 1999.
  Amended and Restated Certificate of Incorporation filed on August 16, 1999.
 Second Amended and Restated Certificate of Incorporation filed on August 31,
                                     1999.





     divine interVentures, inc. (the "Corporation"), a corporation organized and
existing under, and by virtue of, the General Corporation Law of the State of
Delaware (the "DGCL"), does hereby certify that this Amended and Restated
Certificate of Incorporation of the Corporation (the "Certificate of
Incorporation") set forth below has been duly adopted in accordance with
Sections 242 and 245 of the DGCL.


                                   ARTICLE I
                                   ---------

     The name of the Corporation is divine interVentures, inc.


                                  ARTICLE II
                                  ----------

     The address of the Corporation's registered office in the State of Delaware
is 30 Old Rudnick Lane, Suite 100, Dover, Delaware 19901 in the county of Kent.
The name of the Corporation's registered agent at such address is Lexis Document
Services Inc.


                                  ARTICLE III
                                  -----------

     The nature of the business to be conducted or promoted by the Corporation
is to engage in any lawful act or activity for which corporations may be
organized under the DGCL.


                                  ARTICLE IV
                                  ----------

     A.   Authorized Capital Stock.  Effective upon the filing of this
          ------------------------
Certificate of Incorporation, the total number of shares of capital stock of all
classes which the Corporation shall have authority to issue is 2,650,000,000
shares, which shall be divided as follows:  (i)  2,500,000,000 shares of Class A
Common Stock, par value $0.001 per share ("Class A Common Stock"), (ii)
100,000,000 shares of Class C Common Stock, par value $0.001 per share ("Class C
Common Stock") and (iii) 50,000,000 shares of Preferred Stock, par value $0.001
per share ("Preferred Stock").  "Common Stock," when used herein, shall mean the
Class A Common Stock and the Class C Common Stock together.
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     B.   Common Stock. The relative powers, preferences and participating,
          ------------
optional or other special rights, and qualifications, limitations and
restrictions of the Class A Common Stock and Class C Common Stock of the
Corporation shall be as follows:

               1.    Except as otherwise set forth below in this Article IV, the
     relative powers, preferences and participating, optional or other special
     rights, and the qualifications, limitations or restrictions of the Class A
     Common Stock and Class C Common Stock shall be identical in all respects.

               2.    Subject to the rights of the holders of any outstanding
     Preferred Stock and subject to any other provisions of this Certificate of
     Incorporation, holders of Class A Common Stock and Class C Common Stock
     shall be entitled to receive such dividends and other distributions in
     cash, stock of any corporation or, subject to the next sentence, shares of
     Common Stock of the Corporation or any property of the Corporation as may
     be declared thereon by the Board of Directors of the Corporation (the
     "Board of Directors") from time to time out of assets or funds of the
     Corporation legally available therefor and shall share equally on a per
     share basis in all such dividends and other distributions. In the case of
     dividends or other distributions payable in Common Stock, including
     distributions pursuant to stock splits or divisions of Common Stock, only
     shares of Class A Common Stock shall be paid or distributed with respect to
     Class A Common Stock and only shares of Class C Common Stock shall be paid
     or distributed with respect to Class C Common Stock. The shares of Class A
     Common Stock and Class C Common Stock so distributed shall be equal in
     number on a per share basis. Neither the shares of Class A Common Stock nor
     the shares of Class C Common Stock may be reclassified, subdivided or
     combined unless such reclassification, subdivision or combination occurs
     simultaneously and in the same proportion for each class.

               3.    At every meeting of the stockholders of the Corporation,
     every holder of Class A Common Stock shall be entitled to one (1) vote per
     person or by proxy for each share of Class A Common Stock standing in such
     holder's name on the transfer books of the Corporation in connection with
     the election of directors and all other matters submitted to a vote of
     stockholders. Except as may be otherwise required by law, the holders of
     Class C Common Stock shall not be entitled to vote.

               4.    In the event of any dissolution, liquidation or winding up
     of the affairs of the Corporation, whether voluntary or involuntary, after
     payment in full of the amounts required to be paid to the holders of any
     Preferred Stock, the remaining assets and funds of the Corporation shall be
     distributed pro rata to the holders of Class A Common Stock and Class C
     Common Stock. For purposes of this Article IV, Section B.4., the voluntary
     sale, conveyance, lease, exchange or transfer (for cash, shares of stock,
     securities or other consideration) of all or substantially all of the
     assets of the Corporation or a consolidation or merger of the Corporation
     with one or more other corporations (whether or not the Corporation is the
     corporation surviving such consolidation or merger) shall not be deemed to
     be a liquidation, dissolution or winding up, voluntary or involuntary.

                                       2
<PAGE>

               5.    In the case of any reorganization or consolidation or
     merger of the Corporation with one or more other entities, each holder of a
     share of Class A Common Stock shall be entitled to receive with respect to
     such share the same kind and amount of shares of stock and other securities
     and property (including cash), if any, receivable upon such reorganization,
     consolidation or merger by each holder of a share of Class C Common Stock,
     and each holder of a share of Class C Common Stock shall be entitled to
     receive with respect to such share the same kind and amount of shares of
     stock and other securities and property (including cash), if any,
     receivable upon such reorganization, consolidation or merger by a holder of
     a share of Class A Common Stock, except that shares of stock or other
     securities receivable upon such reorganization, consolidation or merger by
     a holder of a share of Class C Common Stock may differ from the shares of
     stock or other securities receivable upon such reorganization,
     consolidation or merger by a holder of a share of Class A Common Stock to
     the extent that the Class A Common Stock and Class C Common Stock differ as
     provided in this Certificate of Incorporation.

               6.    (a)  Each record holder of shares of Class C Common Stock
     may convert such shares into an equal number of shares of Class A Common
     Stock by surrendering the certificates for such shares, accompanied by any
     required tax transfer stamps and by a written notice from such record
     holder to the Corporation stating that such record holder desires to
     convert such shares of Class C Common Stock into the same number of shares
     of Class A Common Stock and requesting that the Corporation issue all of
     such shares of Class A Common Stock to persons named therein, and setting
     forth the number of shares of Class A Common Stock to be issued to each
     such person and the denominations in which the certificates therefor are to
     be issued. To the extent permitted by law, such voluntary conversion shall
     be deemed to have been effected at the close of business on the date of
     such surrender.

                     (b)  The Corporation shall at all times reserve and keep
     available, out of its authorized but unissued Common Stock, such number of
     shares of Class A Common Stock as would be issuable upon the conversion of
     all shares of Class C Common Stock then outstanding.

     C.  Preferred Stock.  The Preferred Stock may be issued from time to time
         ---------------
in one or more series.  Subject to the other provisions of this Certificate of
Incorporation and any limitations prescribed by law, the Board of Directors is
authorized to provide for the issuance of, and issue, shares of Preferred Stock
in series and, by filing a certificate pursuant to the laws of the State of
Delaware, to establish from time to time the number of shares to be included in
each such series and to fix the designation, powers, preferences and rights of
the shares of each such series and any qualifications, limitations or
restrictions thereof.  The number of authorized shares of Preferred Stock may be
increased or decreased (but not below the number of shares thereof then
outstanding) by the affirmative vote of the holders of a majority of the total
voting power of the Common Stock, without a vote of the holders of any of the
Preferred Stock, or of any series thereof, unless a vote of any such holders is
required pursuant to the certificate or certificates establishing such series of
Preferred Stock.

                                       3
<PAGE>

                                   ARTICLE V
                                   ---------

     The business and affairs of the Corporation shall be managed by, or under
the direction of, a board of directors consisting of not less than three (3) nor
more than fifty-nine (59) directors.  The exact number shall be determined from
time to time by resolution adopted by the affirmative vote of a majority of the
directors in office at the time of adoption of such resolution.

     The directors shall be divided into three classes, Class I, Class II and
Class III with each class having as equal a number of members as reasonably
possible.  The initial term of office of the Class I, Class II and Class III
directors shall expire at the annual meeting of stockholders of the Corporation
in 2000, 2001 and 2002, respectively.  Beginning in 2000, at each annual meeting
of stockholders of the Corporation, successors to the class of directors whose
term expires at that annual meeting shall be elected for a three-year term.  If
the number of directors is changed, any increase or decrease shall be
apportioned among the classes by the Board of Directors so as to maintain the
number of directors in each class as nearly equal as is reasonably possible, and
any additional director of any class elected to fill a vacancy resulting from an
increase in such class shall hold office for a term that shall coincide with the
remaining term of that class.  In no case will a decrease in the number of
directors shorten the term of any incumbent director, even though such decrease
may result in an inequality of the classes until the expiration of such term.  A
director shall hold office until the annual meeting of stockholders of the
Corporation in the year in which his or her term expires and until his or her
successor shall be elected and qualified, subject, however, to prior death,
resignation, retirement or removal from office.  Directors may only be removed
for cause, except as otherwise provided by law, by the holders of at least
sixty-six and two-thirds percent (66 2/3%) of the voting power of the shares
entitled to vote generally in the election of directors.  Except as required by
law or the provisions of this Certificate of Incorporation, all vacancies on the
Board of Directors and newly-created directorships shall be filled by the Board
of Directors.  Any director elected to fill a vacancy not resulting from an
increase in the number of directors shall have the same remaining term as that
of his or her predecessor.

     Notwithstanding the foregoing, whenever the holders of any one or more
classes or series of Preferred Stock issued by the Corporation shall have the
right, voting separately by class or series, to elect directors at an annual or
special meeting of stockholders, the election, term of office, filling of
vacancies and other features of such directorships shall be governed by the
terms of this Certificate of Incorporation and any resolutions of the Board of
Directors applicable thereto, and such directors so elected shall not be divided
into classes pursuant to this Article V.  Notwithstanding anything to the
contrary contained in this Certificate of Incorporation, the affirmative vote of
the holders of at least sixty-six and two-thirds percent (66 2/3%) of the voting
power of the shares entitled to vote generally in the election of directors
shall be required to amend, alter or repeal, or to adopt any provision
inconsistent with, this Article V.


                                  ARTICLE VI
                                  ----------

     A.   Written Consent. Any corporate action required or permitted to be
          ---------------
taken at any annual or special meeting of stockholders may be taken only at a
duly called meeting and may not be taken by written consent of the stockholders
in lieu of a meeting.

                                       4
<PAGE>

     B.   Special Meetings.  Special meetings of stockholders of the Corporation
          ----------------
may be called, upon not less than ten (10) nor more than sixty (60) days'
written notice, only by (i) the Chairman of the Board of Directors, (ii) the
Chief Executive Officer of the Corporation, (iii) the President of the
Corporation or (iv) the Board of Directors pursuant to a resolution approved by
a majority of the Board of Directors.

     C.   Amendment.  Notwithstanding anything contained in this Certificate of
          ---------
Incorporation to the contrary, the affirmative vote of the holders of at least
sixty-six and two-thirds percent (66 2/3%) of the voting power of the shares
entitled to vote generally in the election of directors shall be required to
amend, alter or repeal, or to adopt any provision inconsistent with, this
Article VI.


                                  ARTICLE VII
                                  -----------

     In furtherance and not in limitation of the power conferred by statute, the
Board of Directors is expressly authorized to make, alter, amend or repeal the
By-laws of the Corporation (the "By-laws").  The By-laws may be altered, amended
or repealed, or new By-laws may be adopted, by the Board of Directors in
accordance with the preceding sentence or by the vote of the holders of at least
sixty-six and two-thirds percent (66 2/3%) of the voting power of the shares
entitled to vote generally in the election of directors, provided that, if such
alteration, amendment, repeal or adoption of new By-laws is effected at a duly
called special meeting, notice of such alteration, amendment, repeal or adoption
of new By-laws is contained in the notice of such special meeting.
Notwithstanding anything contained in this Certificate of Incorporation to the
contrary, the affirmative vote of holders of at least sixty-six and two-thirds
percent (66 2/3%) of the voting power of the shares entitled to vote generally
in the election of directors shall be required to amend, alter or repeal, or to
adopt any provision inconsistent with, this Article VII.


                                 ARTICLE VIII
                                 ------------

     A director of the Corporation shall not, in the absence of fraud, be
disqualified by his office from dealing or contracting with the Corporation
either as a vendor, purchaser or otherwise, nor, in the absence of fraud, shall
a director of the Corporation be liable to account to the Corporation for any
profit realized by him or her from or through any transaction or contract of the
Corporation by reason of the fact that such director, or any firm of which such
director is a member, or any corporation of which such director is an officer,
director or stockholder, was interested in such transaction or contract if such
transaction or contract has been authorized, approved or ratified in a manner
provided in the DGCL for authorization, approval or ratification of transactions
or contracts between the Corporation and one or more of its directors or
officers or between the Corporation and any other corporation, partnership,
association or other organization in which one or more of its directors or
officers are directors or officers or have a financial interest.

                                       5
<PAGE>

                                  ARTICLE IX
                                  ----------

     Meetings of stockholders may be held within or without the State of
Delaware as the By-laws may provide.  The books of the Corporation may be kept
outside the State of Delaware at such place or places as may be designated from
time to time by the Board of Directors or in the By-laws.  Election of directors
need not be by written ballot unless the By-laws so provide.

                                   ARTICLE X
                                   ---------

     Whenever a compromise or arrangement is proposed between the Corporation
and its creditors or any class of them and/or between the Corporation and its
stockholders or any class of them, any court of equitable jurisdiction within
the State of Delaware may, on the application in a summary way of the
Corporation or of any creditor or stockholder thereof or on the application of
any receiver or receivers appointed for the Corporation under the provisions of
Section 291 of the DGCL or on the application of trustees in dissolution or of
any receiver or receivers appointed for the Corporation under the provisions of
Section 279 of the DGCL, order a meeting of the creditors or class of creditors
and/or the stockholders or class of stockholders of the Corporation, as the case
may be, to be summoned in such manner as said court directs.  If a majority in
number representing three-fourths (3/4) of the value of the creditors or class
of creditors and/or the stockholders or class of stockholders of the
Corporation, as the case may be, agree to any compromise or arrangement or to
any reorganization of the Corporation as a consequence of such compromise or
arrangement, said compromise, arrangement or reorganization shall, if sanctioned
by the court to which said application has been made, be binding on all the
creditors or class of creditors and/or on all the stockholders or class of
stockholders, of the Corporation, as the case may be, and also on the
Corporation.


                                  ARTICLE XI
                                  ----------

     The Board of Directors may adopt a resolution proposing to amend, alter,
change or repeal any provision contained in this Certificate of Incorporation,
in the manner now or hereafter prescribed by statute.


                                  ARTICLE XII
                                  -----------

     A.    Indemnification of Officers and Directors:  The Corporation shall:
           -----------------------------------------

               1.    indemnify, to the fullest extent permitted by the DGCL, any
     present or former director of the Corporation, and may indemnify any
     present or former officer, employee or agent of the Corporation selected
     by, and to the extent determined by, the Board of Directors for
     indemnification (such selection to be evidenced by an indemnification
     agreement), who was or is a party or is threatened to be made a party to
     any threatened, pending or completed action, suit or proceeding, whether
     civil, criminal, administrative or investigative (other than an action by,
     or in the right of, the Corporation) by reason of the fact that such person
     is or was a director, or is or was serving at the request of the
     Corporation as a director, officer, employee or agent of

                                       6
<PAGE>

     another corporation, partnership, joint venture, trust or other enterprise,
     or if such person has previously been designated for indemnification by a
     resolution of the Board of Directors, is or was an officer, employee or
     agent of the Corporation, against expenses (including attorneys' fees),
     judgments, fines and amounts paid in settlement actually and reasonably
     incurred by such person in connection with such action, suit or proceeding
     if such person acted in good faith and in a manner such person reasonably
     believed to be in or not opposed to the best interests of the Corporation
     and, with respect to any criminal action or proceeding, had no reasonable
     cause to believe such person's conduct was unlawful. The termination of any
     action, suit or proceeding by judgment, order, settlement or conviction, or
     upon a plea of nolo contendere or its equivalent, shall not, of itself,
     create a presumption that the person did not act in good faith and in a
     manner which such person reasonably believed to be in, or not opposed to,
     the best interests of the Corporation and, with respect to any criminal
     action or proceeding, had reasonable cause to believe that such person's
     conduct was unlawful; and

               2.    indemnify any present or former director of the
     Corporation, and may indemnify any present or former officer, employee or
     agent of the Corporation selected by, and to the extent determined by, the
     Board of Directors for indemnification (such selection to be evidenced by
     an indemnification agreement), who was or is a party or is threatened to be
     made a party to any threatened, pending or completed action or suit by, or
     in the right of, the Corporation to procure a judgment in its favor by
     reason of the fact that such person is or was a director, or is or was
     serving at the request of the Corporation as a director, officer, employee
     or agent of another corporation, partnership, joint venture, trust or other
     enterprise, or if such person has previously been designated for
     indemnification by a resolution of the Board of Directors, is or was an
     officer, employee or agent of the Corporation, against expenses (including
     attorneys' fees) actually and reasonably incurred by such person in
     connection with the defense or settlement of such action or suit if such
     person acted in good faith and in a manner such person reasonably believed
     to be in, or not opposed to, the best interests of the Corporation, except
     that no indemnification shall be made in respect of any claim, issue or
     matter as to which such person shall have been adjudged to be liable to the
     Corporation, unless and only to the extent that the Court of Chancery or
     the court in which such action or suit was brought shall determine upon
     application that, despite the adjudication of liability but in view of all
     the circumstances of the case, such person is fairly and reasonably
     entitled to indemnity for such expenses which the Court of Chancery or such
     other court shall deem proper; and

               3.    indemnify any present or former director or officer, and
     may indemnify any present or former employee or agent of the Corporation
     selected by, and to the extent determined by, the Board of Directors for
     indemnification (such selection to be evidenced by an indemnification
     agreement), against expenses (including attorneys' fees) actually and
     reasonably incurred by such person in connection therewith, to the extent
     that such person has been successful on the merits or otherwise in defense
     of any action, suit or proceeding referred to in Article XII.A.1. and 2.,
     or in defense of any claim, issue or matter therein; and

               4.    pay expenses incurred by a director, or an officer who is
     entitled to

                                       7
<PAGE>

     indemnification hereunder, in defending a civil or criminal action, suit or
     proceeding in advance of the final disposition of such action, suit or
     proceeding upon receipt of an undertaking by or on behalf of such director
     or officer to repay such amount if it shall ultimately be determined that
     such director or officer is not entitled to be indemnified by the
     Corporation as authorized in this Article XII; and

               5.    notwithstanding the foregoing provisions and except as
     required by the DGCL, the Corporation shall not be obligated to indemnify
     or pay expenses incurred by any person with respect to any threatened,
     pending, or completed claims, suits or actions, whether civil, criminal,
     administrative, investigative or otherwise ("Proceedings"), initiated or
     brought voluntarily by such person and not by way of defense (other than
     Proceedings brought to establish or enforce a right to indemnification
     under the provisions of this Article XII, unless a court of competent
     jurisdiction determines that each of the material assertions made by such
     person in such Proceedings were not made in good faith or were frivolous).
     The Corporation shall not be obligated to indemnify such person for any
     amount paid in settlement of a Proceeding covered hereby without the prior
     written consent of the Corporation to such settlement; and

               6.    not deem the indemnification and advancement of expenses
     provided by, or granted pursuant to, the other subsections of this Article
     XII as exclusive of any other rights to which those seeking indemnification
     or advancement of expenses may be entitled under any By-law, agreement or
     vote of stockholders or disinterested directors, or otherwise (including
     with respect to directors and officers, as to action in such director's or
     officer's official capacity and as to action in another capacity while
     holding such office); and

               7.    have the right, authority and power to purchase and
     maintain insurance on behalf of any person who is or was a director,
     officer, employee or agent of the Corporation, or is or was serving at the
     request of the Corporation as a director, officer, employee or agent of
     another corporation, partnership, joint venture, trust or other enterprise
     against any liability asserted against such person and incurred by such
     person in any such capacity, or arising out of such person's status as
     such, whether or not the Corporation would have the power to indemnify such
     person against such liability under the provisions of this Article XII; and

               8.    deem the provisions of this Article XII to be a contract
     between the Corporation and each director, and each appropriately
     designated officer, employee or agent, who serves in such capacity at any
     time while this Article XII is in effect, and any repeal or modification of
     this Article XII shall not affect any rights or obligations then existing
     with respect to any state of facts then or theretofore existing or any
     action, suit or proceeding theretofore or thereafter brought or threatened
     based in whole or in part upon such state of facts. The provisions of this
     Article XII shall not be deemed to be a contract between the Corporation
     and any directors, officers, employees or agents of any other corporation
     (the "Second Corporation") which shall merge into or consolidate with the
     Corporation when the Corporation shall be the surviving or resulting
     corporation, and any such directors, officers, employees or agents of the
     Second Corporation shall be indemnified to the extent required under the
     DGCL only at the discretion of the Board of

                                       8
<PAGE>

     Directors; and

               9.    continue the indemnification and advancement of expenses
     provided by, or granted pursuant to, this Article XII, unless otherwise
     provided when authorized or ratified, as to a person who has ceased to be a
     director, officer, employee or agent of the Corporation, and the
     indemnification and advancement of expenses provided by, or granted
     pursuant to, this Article XII shall inure to the benefit of the heirs,
     executors and administrators of such person.

     B.  Elimination of Certain Liability of Directors:  No director of the
         ---------------------------------------------
Corporation shall be personally liable to the Corporation or its stockholders
for monetary damages for breach of fiduciary duty as a director, except for
liability (i) for any breach of the director's duty of loyalty to the
Corporation or its stockholders, (ii) for acts or omissions not in good faith or
which involve intentional misconduct or a knowing violation of law, (iii) under
Section 174 of the DGCL, as the same exists or hereafter may be amended, or (iv)
for any transaction from which the director derived an improper personal
benefit.  If the DGCL is amended to authorize the further elimination or
limitation of liability of directors, then the liability of a director of the
Corporation, in addition to the limitation on personal liability provided
herein, shall be limited to the fullest extent permitted by the amended DGCL.
Any repeal or modification of this Article XII by the stockholders of the
Corporation shall be prospective only and shall not adversely affect any
limitation on the personal liability of a director of the Corporation existing
at the time of such repeal or modification.

                                       9
<PAGE>

     IN WITNESS WHEREOF, the Corporation has caused this Third Amended and
Restated Certificate of Incorporation to be signed by its Chairman of the Board
and Chief Executive Officer, on July 18, 2000.

                                    DIVINE INTERVENTURES, INC.


                                    By:/s/ANDREW J. FILIPOWSKI
                                       -----------------------------------
                                          Andrew J. Filipowski
                                          Chairman of the Board and Chief
                                          Executive Officer