<PAGE>

                                                                    Exhibit 10.3
                                                                    ------------

THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE BEEN ACQUIRED FOR INVESTMENT
AND HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED.  SUCH
SECURITIES MAY NOT BE SOLD OR TRANSFERRED IN THE ABSENCE OF SUCH REGISTRATION
UNLESS THE COMPANY RECEIVES AN OPINION OF COUNSEL REASONABLY ACCEPTABLE TO IT
STATING THAT SUCH SALE OR TRANSFER IS EXEMPT FROM REGISTRATION AND PROSPECTUS
DELIVERY REQUIREMENTS OF SUCH ACT.

THE SECURITIES REPRESENTED BY THIS CERTIFICATE ARE SUBJECT TO CERTAIN
RESTRICTIONS UPON TRANSFER AND RIGHTS OF FIRST REFUSAL AND MAY BE TRANSFERRED
ONLY IN ACCORDANCE WITH THE TERMS OF AN AGREEMENT BETWEEN THE COMPANY AND THE
REGISTERED HOLDER, A COPY OF WHICH IS ON FILE AT THE PRINCIPAL OFFICE OF THE
COMPANY.

                            PREFERRED STOCK WARRANT
                                       of
                                enCOMMERCE, INC.

D - 1                                                             370,000 Shares

     THIS CERTIFIES THAT, for value received, the sufficiency of which is hereby
acknowledged, Andersen Consulting LLP ("AC" or the "Warrantholder"), is
entitled, on the terms and subject to conditions set forth below, to subscribe
for and purchase from enCommerce, Inc., a California corporation (the
"Company"), at the Warrant Price defined in Section 2 below, 370,000 fully paid
and non-assessable shares of the Company's Series D Preferred Stock (the
"Warrant Shares"), such price and such number of shares being subject to
adjustment upon occurrence of the contingencies set forth in this Warrant.  AC
and the Company acknowledge and agree that 70,000 of the Warrant Shares subject
to this Warrant are consideration for the entering into of the AC Consulting
Agreement, and 300,000 of the Warrant Shares subject to the Warrant are
consideration for the entering into the Master Alliance Agreement.

     Upon delivery of this Warrant (with the Notice of Exercise in the form
attached as Attachment A), together with payment of the Warrant Price for the
            ------------
shares of the Company's Series D Preferred Stock (the "Series D Preferred")
thereby purchased, which payment may be made by converting this Warrant, or any
portion thereof, pursuant to Section 3 below ("Warrant Conversion"), at the
principal office of the Company or at such other office or agency as the Company
may designate by notice in writing to the holder hereof, the holder of this
Warrant shall be entitled to receive a certificate or certificates for the
shares of Series D Preferred so purchased.  All shares of Series D Preferred
which may be issued upon the exercise of this Warrant will, upon issuance, be
fully paid and non-assessable and free from all taxes, liens and charges with
respect thereto.

     This Warrant is subject to the following terms and conditions:
<PAGE>

        1.  Term of Warrant.  This Warrant may be exercised in whole or in part,
            ---------------
at any time after issuance and prior to 5:00 p.m., PST, April 11, 2003 (the
"Term"). Upon the expiration of the Term, this Warrant, to the extent not
exercised, shall terminate.

        2.  Warrant Price.  The exercise price of this Warrant (the "Warrant
            -------------
Price") shall equal $9.46 per share, subject to adjustment as provided in
Section 4 below.

        3.  Method of Exercise.
            ------------------

            (i) Cash Exercise.  The purchase rights represented by this Warrant
                -------------
may be exercised by the Warrantholder, in whole, or in part, by the surrender of
this Warrant (with the duly executed Notice of Exercise attached as Attachment
                                                                    ----------
A) at the principal office of the Company, and by the payment to the Company, by
certified or cashier's check or other check acceptable to the Company, of an
amount equal to the aggregate Warrant Price of the Warrant Shares being
purchased.

           (ii) Net Issue Exercise.  In lieu of exercising this Warrant for cash
                ------------------
under clause (i), in the event that the Company's securities are listed on the
Nasdaq National Market, the Warrantholder may elect (provided that the election
occurs 180 days after the effective date of the Company's initial public
offering) to receive Warrant Shares equal to the value of this Warrant (or the
portion thereof being canceled) by surrender of this Warrant at the principal
office of the Company and specification of such election on the Notice of
Election, in which event the Company shall issue to the Warrantholder a number
of Warrant Shares computed using the following formula:

     X = Y(A-B)
         ------
           A

Where     X  = the number of Warrant Shares to be issued to the Warrantholder.

          Y  =  the number of Warrant Shares for which this Warrant is then
                 being exercised.

          A  =  the fair market value of one share of the Company's Common
                 Stock.

          B  =  the Warrant Price (as adjusted to the date of such calculation).

     (iii)  Fair Market Value.  For purposes of this Section 3, the fair market
            -----------------
value of the Company's Common Stock shall mean the average of the closing bid
and asked prices of the Company's Common Stock quoted on the Nasdaq National
Market, or the closing prices quoted on any exchange on which the Common Stock
is listed, whichever is applicable, as published in the Western Edition of The
                                                                           ---
Wall Street Journal for the ten (10) trading days prior to the date of
-------------------
determination of fair market value.

     4.  Vesting.  The Warrant shall be exercisable according to the following
         -------
vesting schedule: 300,000 Warrant Shares shall vest immediately upon the
execution by the Company and

                                      -2-
<PAGE>

AC of the Market Alliance Agreement and 70,000 Warrant Shares shall vest
immediately upon the execution by the Company and AC of the Consulting
Agreement.

      5.  Adjustment of Warrant Price and Number of Warrant Shares.
          --------------------------------------------------------

          The number and kind of Warrant Shares purchasable upon the exercise of
this Warrant and the Warrant Price shall be subject to adjustment from time to
time in accordance with the following provisions:

          (a)  Reclassification, Consolidation, Merger, etc.  In case of any
               --------------------------------------------
reclassification, exchange, substitution or change of outstanding securities of
the class issuable upon exercise of this Warrant (other than as a result of a
subdivision or combination), or in case of any consolidation or merger of the
Company with or into another corporation, or the sale, transfer or lease of all
or substantially all of the assets of the Company, the Company, or such
successor corporation, as the case may be, shall execute a new Warrant,
providing that the holder of this Warrant shall have the right to exercise such
new Warrant, and procure upon such exercise in lieu of each Warrant Share
previously issuable upon exercise of this Warrant, the kind and amount of shares
of stock, other securities, money and property receivable upon such
reclassification, exchange, substitution, change, consolidation, merger, sale,
transfer or lease by a holder of one Warrant Share immediately prior to such
event. Such new Warrant shall provide for adjustments which shall be as nearly
equivalent as may be practicable to the adjustments provided for in this Section
4. The provisions of this paragraph (a) shall similarly apply to successive
reclassifications, exchanges, substitutions, changes, consolidations, mergers,
sales, transfers or leases.

          (b)  Conversion of the Series D Preferred. In the event all of the
shares of Series D Preferred are, or if outstanding would be, at any time prior
to the expiration of this Warrant, converted into shares of the Company's Common
Stock (whether due to the IPO or otherwise), then this Warrant shall immediately
become exercisable for that number of shares of the Company's Common Stock equal
to the number of shares of the Common Stock that would have been received if
this Warrant had been exercised in full and shares of the Series D Preferred
received thereupon had been simultaneously converted, and the Warrant Price
shall be immediately adjusted to equal the product obtained by multiplying the
Warrant Price in effect immediately prior to such conversion by a fraction, the
numerator of which shall be the number of shares of Series D Preferred for which
this Warrant was exercisable immediately prior to such conversion and the
denominator of which shall be the number of shares of Common Stock for which
this Warrant is exercisable immediately after such conversion.

          (c)  Subdivision, Stock Dividend or Combination of Shares.  If the
               ----------------------------------------------------
Company at any time while this Warrant remains outstanding and unexpired shall
subdivide or combine the Series D Preferred, or shall issue a stock dividend
with respect to the Series D Preferred, the Warrant Price shall be
proportionately decreased in the case of a subdivision or stock dividend or
increased in the case of a combination.

          (d)  Adjustment of Number of Shares.  Upon each adjustment in the
               ------------------------------
Warrant Price for subdivisions or combinations as contemplated under paragraph
(b) above, the number of shares

                                      -3-
<PAGE>

of Series D Preferred purchasable hereunder shall be adjusted, to the nearest
whole share, to the product obtained by multiplying the number of shares
purchasable immediately prior to such adjustment in the Warrant Price by a
fraction, the numerator of which shall be the Warrant Price immediately prior to
such adjustment and the denominator of which shall be the Warrant Price
immediately thereafter.

         (e)  No Impairment.  The Company shall not, by amendment of its
              -------------
Articles of Incorporation or through a reorganization, transfer of assets,
consolidation, merger, dissolution, issue, or sale of securities or any other
voluntary action, avoid or seek to avoid the observance or performance of any of
its terms to be observed or performed under this Warrant by the Company, but
shall at all times in good faith assist in carrying out of all the provisions of
this Section 4 and in taking all such action as may be necessary or appropriate
to protect the Warrantholder's rights under this Section 4 against impairment.
If the Company takes any action affecting the Series D Preferred other than as
described above that adversely affects Warrantholder's rights under this
Warrant, the Warrant Price shall be adjusted downward.

     6.  Reservation of Stock.  On and after the date hereof, the Company will
         --------------------
reserve from its authorized and unissued (i)  Series D Preferred a sufficient
number of shares to provide for the issuance of the Warrant Shares upon the
exercise of this Warrant and (ii) Common Stock a sufficient number of shares for
issuance upon conversion of the Warrant Shares.

     7.  Notices.
         -------

         (a)  Upon any adjustment of the Warrant Price and any increase or
decrease in the number of shares of Series D Preferred purchasable upon the
exercise of this Warrant, then the Company shall give written notice of such
adjustment promptly thereafter to the registered holder of this Warrant (the
"Notice"). The Notice shall be mailed to the address of such holder as shown on
the books of the Company and shall state the Warrant Price as adjusted and the
increased or decreased number of shares purchasable upon the exercise of this
Warrant, setting forth in reasonable detail the method of calculation of each.

         (b)  In the event that the Company shall propose at any time to effect
an initial public offering, the Company shall send to the Warrantholder at least
ten (10) days' prior written notice of the date when the same shall take place.

         8.  Miscellaneous.
             -------------

             (a)  The terms of this Warrant shall be binding upon and shall
inure to the benefit of any successors or assigns of the Company and of any
permitted assigns of the Warrantholder. This Warrant may be transferred or
assigned by the Warrantholder only in compliance with Section 3 of that certain
Amended and Restated Shareholder Rights Agreement, dated February 10, 2000, as
the same may be amended from time to time, by and between the Company, the
Warrantholder and the other parties thereto.

                                      -4-
<PAGE>

             (b)  Other than as provided herein, no holder of this Warrant, as
such, shall be entitled to vote or receive dividends or be deemed to be a
shareholder of the Company for any purpose, nor shall anything contained in this
Warrant be construed to confer upon the holder of this Warrant, as such, any
rights of a shareholder of the Company or any right to vote, give or withhold
consent to any corporate action, receive notice of meetings, receive dividends
or subscription rights, or otherwise.

            (c)  Receipt of this Warrant by the holder hereof shall constitute
acceptance of and agreement to the foregoing terms and conditions.

            (d)  Upon receipt of evidence reasonably satisfactory to the Company
of the loss, theft, destruction or mutilation of this Warrant and, in the case
of any such loss, theft or distribution, upon delivery of an indemnity agreement
reasonably satisfactory in form and amount to the Company or, in the case of any
such mutilation, upon surrender and cancellation of such Warrant, the Company at
its expense will execute and deliver, in lieu thereof, a new Warrant of like
date and tenor.

            (e)  Any provision of this Warrant may be amended, waived or
modified upon the written consent of the Company and the holders of a majority
of the Warrant Shares issued or issuable upon exercise of this Warrant or any
successor warrant(s).

            (f)  This Warrant shall be governed by the internal substantive
laws, but not the choice of law rules, of the State of California.

                                      -5-
<PAGE>

     IN WITNESS WHEREOF, the Company has caused this Warrant to be signed by its
duly authorized officer.

Dated:  April 11, 2000


                                    enCommerce, Inc.

                                    /s/ Alberto Yepez
                                    ---------------------------------
                                    J. Alberto Yepez

                                      -6-
<PAGE>

                                  ATTACHMENT A
                                  ------------

                               NOTICE OF EXERCISE
                               ------------------


     TO:  enCommerce, Inc.
          2901 Patrick Henry Drive
          Santa Clara, CA  95054
          Attn:  President

     1.   The undersigned hereby elects to purchase ___________ shares of the
Series D Preferred of enCOMMERCE, INC. pursuant to the terms of the attached
Warrant, and tenders herewith payment of the purchase price of such shares in
full, together with all applicable transfer taxes, if any.

     2.   Please issue a certificate or certificates representing such shares of
Series D Preferred in the name of the undersigned or in such other name as is
specified below:

                       _________________________________
                                     (Name)

                       _________________________________

                       _________________________________
                                   (Address)

     3.  The undersigned represents that the above shares of Series D Preferred
are being acquired for the account of the undersigned for investment and not
with a view to, or for resale in connection with, the distribution thereof and
that the undersigned has no present intention of distributing or reselling such
shares. In support thereof, the undersigned has executed the Investment
Representation Statement attached as Exhibit A.
                                     ---------

                                    Signature of Warrantholder:

                                    Andersen Consulting LLP

                                    --------------------------------------

                                    By:
                                       -----------------------------------

                                    Title:
                                          --------------------------------

                                    Date:
                                         ---------------------------------
<PAGE>

                                   EXHIBIT A
                                   ---------

THIS STATEMENT MUST BE COMPLETED, SIGNED AND RETURNED TO enCOMMERCE, INC. ALONG
WITH THE NOTICE OF EXERCISE BEFORE THE SERIES D PREFERRED ISSUABLE UPON EXERCISE
OF THE ATTACHED WARRANT WILL BE ISSUED.

                                enCOMMERCE, INC.

                                WARRANT EXERCISE

                      INVESTMENT REPRESENTATION STATEMENT

PURCHASER           :

COMPANY             :  enCommerce, Inc.

SECURITY            :  Series D Preferred

NUMBER OF SHARES    :

DATE                :  _______________, 20__

     In connection with the purchase of the above-listed Securities, the
Purchaser represents to the Company the following:

     (a)  It has substantial experience in evaluating and investing in private
placement transactions of securities in companies similar to the Company so that
it is capable of evaluating the merits and risks of its investment in the
Company and has the capacity to protect its own interests. It acknowledges that
its investment in the Company is highly speculative and entails a substantial
degree of risk and it is in a position to lose the entire amount of such
investment.

     (b)  It is acquiring the Securities for investment for its own account, not
as a nominee or agent, and not with the view to, or for resale in connection
with, any distribution thereof. It understands that the Securities have not
been, and will not be, registered under the Securities Act of 1933, as amended
(the "Securities Act") by reason of a specific exemption from the registration
provisions of the Securities Act, the availability of which depends upon, among
other things, the bona fide nature of the investment intent and the accuracy of
                  ---- ----
its representations as expressed herein. It is an "accredited investor" within
the meaning of Regulation D, Rule 501(a), promulgated by the Securities and
Exchange Commission (the "SEC").

     (c)  It acknowledges that the Securities must be held indefinitely unless
subsequently registered under the Securities Act or unless an exemption from
such registration is available. It is aware of the provisions of Rule 144
promulgated under the Securities Act which permit limited resale of shares
purchased in a private placement subject to the satisfaction of certain
conditions, including, among other things, the existence of a public market for
the shares, the
<PAGE>

availability of certain current public information about the Company, the resale
occurring not less than one year after a party has purchased and paid for the
security to be sold, the sale being effected through a "broker's transaction" or
in transactions directly with a "market maker" and the number of shares being
sold during any three-month period not exceeding specified limitations.

          (d)  It understands that no public market now exists for any of the
     Securities and that the Company has made no assurances that a public
     market will ever exist for the Securities.

          (e)  It has had an opportunity to discuss the Company's business,
     management and financial affairs with its management. It has also had an
     opportunity to ask questions of officers of the Company, which questions
     were answered to its satisfaction. It understands that such discussions, as
     well as any written information issued by the Company, were intended to
     describe certain aspects of the Company's business and prospects but were
     not a thorough or exhaustive description. It acknowledges that any business
     plans prepared by the Company have been and continue to be subject to
     change and that any projections included in such business plans are
     necessary speculative in nature, and it can be expected that some or all of
     the assumptions of the projections will not materialize or will vary
     significantly from actual results.

          (f)  It understands that the certificates evidencing the Securities
     will be imprinted with a legend which prohibits the transfer of the
     Securities unless they are registered or such registration is not required
     in the opinion of counsel for the Purchaser reasonably satisfactory to the
     Company or unless the Company receives a no-action letter from the SEC.

          The following legends will be placed on the certificate(s) for the
     Securities, or any substitutions therefor:

          THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE BEEN ACQUIRED FOR
          INVESTMENT AND HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF
          1933, AS AMENDED.  SUCH SECURITIES MAY NOT BE SOLD OR TRANSFERRED IN
          THE ABSENCE OF SUCH REGISTRATION UNLESS THE COMPANY RECEIVES AN
          OPINION OF COUNSEL REASONABLY ACCEPTABLE TO IT STATING THAT SUCH SALE
          OR TRANSFER IS EXEMPT FROM THE REGISTRATION AND PROSPECTUS DELIVERY
          REQUIREMENTS OF SUCH ACT.

          THE SECURITIES REPRESENTED BY THIS CERTIFICATE ARE SUBJECT TO CERTAIN
          RESTRICTIONS UPON TRANSFER AND RIGHTS OF FIRST REFUSAL AND MAY BE
          TRANSFERRED ONLY IN ACCORDANCE WITH THE TERMS OF AN AGREEMENT BETWEEN
          THE COMPANY AND THE REGISTERED HOLDER, A COPY OF WHICH IS ON FILE AT
          THE PRINCIPAL OFFICE OF THE COMPANY.

          (g)  In accepting the transfer of the above-listed Securities, it
     agrees to be bound by the terms and conditions of that certain Amended and
     Restated Shareholder Rights Agreement,

                                      -2-
<PAGE>

     dated February 10, 2000, as the same may be amended from time to time, by
     and between the Company, the Purchasers and certain Common Shareholders
     (each as defined in such Agreement).

                                    Signature of Purchaser:

                                    ANDERSEN CONSULTING, LLP

                                    ---------------------------------

                                    By:
                                       ------------------------------

                                    Title:
                                          ---------------------------

                                    Date:
                                         ----------------------------

                                      -3-