<PAGE>

                                                                     EXHIBIT 4.6

THE SECURITIES REPRESENTED BY THIS INSTRUMENT HAVE NOT BEEN REGISTERED UNDER THE
SECURITIES ACT OF 1933, AS AMENDED, OR QUALIFIED UNDER APPLICABLE STATE
SECURITIES LAWS AND HAVE BEEN TAKEN FOR INVESTMENT PURPOSES ONLY AND NOT WITH A
VIEW TO OR FOR SALE IN CONNECTION WITH ANY DISTRIBUTION THEREOF. THE SECURITIES
MAY NOT BE SOLD OR OTHERWISE TRANSFERRED IN THE ABSENCE OF SUCH REGISTRATION AND
QUALIFICATION WITHOUT, EXCEPT UNDER CERTAIN SPECIFIC LIMITED CIRCUMSTANCES, AN
OPINION OF COUNSEL FOR THE HOLDER, CONCURRED IN BY COUNSEL FOR THE COMPANY THAT
SUCH REGISTRATION AND QUALIFICATION ARE NOT REQUIRED.

                            CLEARCOMMERCE CORPORATION

                             STOCK PURCHASE WARRANT

    THIS CERTIFIES that Imperial Bank (the "Holder") is entitled, upon the terms
                                            ------
and subject to the conditions hereinafter set forth, at any time on or after the
date of this Warrant and on or prior to February 28, 2004 (the "Expiration
                                                                ----------
Date"), but not thereafter, to subscribe for and purchase from ClearCommerce
----
Corporation a Delaware corporation (the "Company"), 14,144 Shares (as
                                         -------
hereinafter defined). "Shares" shall be the Company's Series C Preferred Stock.
The "Exercise Price" shall be $7.07 per Share. This Warrant is being issued in
     --------------
conjunction with termination of that certain First Amendment to the Credit
Agreement and Promissory Note and Forbearance dated as of September 14, 1999.

1.   Exercise of Warrant.
     -------------------

         (a) Unless earlier terminated under Section 8, the purchase rights
represented by this Warrant are exercisable by the Holder, in whole or in part,
at any time after the date hereof and before the close of business on the
Expiration Date, by the surrender of this Warrant and the Notice of Exercise
annexed hereto duly executed at the principal executive office of the Company
(or such other office or agency of the Company as it may designate by notice in
writing to the Holder at the address of the Holder appearing on the books of the
Company), and upon payment of the Exercise Price of the Shares thereby purchased
(by cash or by check or bank draft payable to the order of the Company in an
amount equal to the Exercise Price of the shares thereby purchased); whereupon
the Holder shall be entitled to receive a certificate for the number of Shares
so purchased. The Company agrees that if at the time of the surrender of this
Warrant and purchase of the Shares, the Holder shall be entitled to exercise
this Warrant, the Shares so purchased shall be and be deemed to be issued to
such holder as the record owner of such Shares as of the close of business on
the date on which this Warrant shall have been exercised as aforesaid.

         (b) Certificates for Shares purchased hereunder shall be delivered to
the Holder within a reasonable time after the date on which this Warrant shall
have been exercised as aforesaid.

         (c) The Company covenants that all Shares that may be issued upon the
exercise of rights represented by this Warrant will, upon exercise of the rights
represented by this Warrant, be
<PAGE>

fully paid and nonassessable and free from all taxes, liens and charges in
respect of the issue thereof (other than taxes in respect of any transfer
occurring contemporaneously with such issue).

2.   Net Exercise.

     (a) In lieu of exercising this Warrant by payment of cash or check, the
Holder may elect to receive shares equal to the value of this Warrant (or the
portion thereof being exercised), at any time after the date hereof and before
the close of business on the Expiration Date, by surrender of this Warrant at
the principal executive office of the Company, together with the Notice of
Conversion annexed hereto, in which event the Company will issue to the Holder
Shares in accordance with the following formula:

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




    Where,        X    =   the number of Shares to be issued to Holder;

                  Y    =   the number of Shares for which the Warrant is being
                           exercised;

                  A    =   the fair market value of one Share; and

                  B    =   the Exercise Price.

     (b) For purposes of this Section 2, the fair market value of a Share is
defined as follows:

         (i) if the exercise is in connection with an initial public offering of
the Common Stock, and if the Company's registration statement relating to such
offering has been declared effective by the Securities and Exchange Commission,
then the fair market value shall be the initial "Price to Public" specified in
the final prospectus with respect to the offering;

         (ii) if the exercise is in connection with a transaction described in
Section 8, then the fair market value shall be the value received pursuant to
such transaction as determined in good faith by the board of directors of the
Company;

         (iii) if the exercise occurs after, and not in connection with the
Company's initial public offering, and:

              (1) if traded on a securities exchange or the Nasdaq Stock Market,
the value shall be deemed to be the average of the closing prices of the
securities on such exchange or market over the 20-day period ending three (3)
days prior to the closing of such transaction; or

              (2) if actively traded over-the-counter, the value shall be deemed
to be the average of the closing bid prices over the 30-day period ending three
(3) days prior to the closing of such transaction;

                                       2
<PAGE>

              (iv) if there is no active public market, the value shall be the
fair market value thereof, as determined in good faith by the board of directors
of the Company.

     3. No Fractional Shares or Scrip. No fractional shares or scrip
        -----------------------------
representing fractional shares shall be issued upon the exercise of this
Warrant. With respect to any fraction of a share called for upon the exercise of
this Warrant, an amount equal to such fraction multiplied by the then current
price at which each Share may be purchased hereunder shall be paid in cash to
the Holder.

     4. Charges, Taxes and Expenses. Issuance of certificates for Shares upon
        ---------------------------
the exercise of this Warrant shall be made without charge to the holder hereof
for any issue or transfer tax or other incidental expense in respect of the
issuance of such certificate, all of which taxes and expenses shall be paid by
the Company, and such certificates shall be issued in the name of the Holder.


     5. No Rights as Shareholders. This Warrant does not entitle the Holder to
        -------------------------
any voting rights or other rights as a shareholder of the Company prior to the
exercise thereof.

     6. Loss, Theft, Destruction or Mutilation of Warrant. Upon receipt by the
        -------------------------------------------------
Company of evidence reasonably satisfactory to it of the loss, theft,
destruction or mutilation of this Warrant, and in case of loss, theft or
destruction, of indemnity or security reasonably satisfactory to it, and upon
reimbursement to the Company of all reasonable expenses incidental thereto, and
upon surrender and cancellation of this Warrant, if mutilated, the Company will
make and deliver a new Warrant of like tenor and dated as of such cancellation,
in lieu of this Warrant.

     7. Saturdays, Sundays, Holidays, etc. If the last or appointed day for the
        ---------------------------------
taking of any action or the expiration of any right required or granted herein
shall be a Saturday or a Sunday or shall be a legal holiday, then such action
may be taken or such right may be exercised on the next succeeding day not a
Saturday, Sunday or a legal holiday.

     8. Automatic Conversion on Merger, etc. If the Company merges with or into
        -----------------------------------
any other corporation or entity, effects a reorganization, or sells or conveys
all or substantially all of its assets to any other corporation or entity in a
transaction in which the shareholders of the Company immediately before the
transaction own immediately after the transaction less than a majority of the
outstanding voting securities of the surviving or corporation or entity (or its
parent), then, unless previously exercised, the Warrant will be deemed to have
been converted immediately prior to the effective date of the transaction
pursuant to Section 2(a) hereof. The Holder will receive certificates
representing the Shares due to the Holder as a result of any such deemed
conversion upon surrender of this Warrant at the principal executive office of
the Company. Notwithstanding the foregoing, if the fair market value of one
Share (as defined in Section 2(b)) is less than the Exercise Price, then the
Warrant shall terminate immediately prior to the effective date.

     9. Adjustments. The Exercise Price and the number of shares purchasable
        -----------
hereunder are subject to adjustment from time to time as follows:

         (a) Reclassification, etc. If the Company, at any time while this
             ---------------------
Warrant, or any portion hereof, remains outstanding and unexpired by
reclassification of securities or otherwise, shall change any of the securities
as to which purchase rights under this Warrant exist into the same or a

                                       3
<PAGE>

different number or securities or any other class or classes, this Warrant shall
thereafter represent the right to acquired such number and kind of securities as
would have been issuable as the result of such change with respect to the
securities that were subject to the purchase rights under this Warrant
immediately prior to such reclassification or other change and the Exercise
Price therefor shall be appropriately adjusted, all subject to further
adjustment as provided in this Section 9.

         (b) Split, Subdivision or Combination of Shares. If the Company at any
             -------------------------------------------
time while this Warrant, or any portion hereof, remains outstanding and
unexpired shall split, subdivide or combine the securities as to which purchase
rights under this Warrant exist, into a different number of securities of the
same class, the Exercise Price for such securities shall be proportionately
decreased in the case of a split or subdivision or proportionately increased in
the case of combination, in both cases by the ratio which the total number of
such securities to be outstanding immediately after such event bears to the
total number of such securities outstanding immediately prior to such event.

         (c) Cash Distributions. No adjustment on account of cash dividends or
             ------------------
interest on the securities as to which purchase rights under this Warrant exist
will be made to the Exercise Price under this Warrant.

     10. Miscellaneous.
         -------------
         (a) Issue Date. The provisions of this Warrant shall be construed and
             ----------
shall be given effect in all respect as if it had been issued and delivered by
the Company on the date set forth below.

         (b) Governing Law. THIS WARRANT SHALL BE GOVERNED IN ALL RESPECTS BY
             -------------
THE LAWS OF THE STATE OF TEXAS AS SUCH LAWS ARE APPLIED TO AGREEMENTS BETWEEN
TEXAS RESIDENTS ENTERED INTO AND TO BE PERFORMED ENTIRELY WITHIN TEXAS.

         (c) Restrictions. By acceptance hereof, the Holder acknowledges that
             ------------
the Shares acquired upon the exercise of this Warrant may have restrictions upon
its resale imposed by state and federal securities laws.

         (d) Waivers and Amendments. This Warrant and any provisions hereof may
             ----------------------
be changed, waived, discharged or terminated only by an instrument in writing
signed by the party against which enforcement of the same is sought.

         (e) Assignment. This Warrant may be assigned or transferred by the
             ----------
Holder only with the prior written approval of the Company; provided, however,
that Holder may transfer all or part of this Warrant to its affiliates,
including, without limitation, Imperial Bancorp, at any time without notice to
the Company, and such affiliate shall then be entitled to all the rights of
Holder under this Warrant and any related agreements. Any affiliate assignee of
Holder shall cooperate fully by delivering, on its own behalf, to the Company
the representations and covenants made by Holder in the Warrant Purchase
Agreement, as requested by the Company, and the Company shall cooperate fully in
ensuring that any stock issued upon exercise of this Warrant is issued in the
name

                                       4
<PAGE>

of the affiliate that exercises the Warrant. This Warrant shall be binding
upon the permitted successors or their assigns of Holder and the Company.

         (f) Construction. The language used in this Warrant will be deemed to
be the language chosen by the parties to express their mutual intent and no
rules of strict construction will be applied against any party.

         (g) Market Stand-off Covenant. The Bank agrees, in connection with the
Company's initial public offering of the Company's securities, (i) not to sell,
make short sales of, loan, grant any options for the purchase of, or otherwise
dispose of any securities of the Company held by the Bank (other than those
shares included in the registration) without the prior written consent of the
Company or the underwriters managing such initial underwritten public offering
of the Company's securities for one hundred eighty (180) days from the effective
date of such registration and (ii) further agrees to execute any agreement
reflecting (i) above as may be requested by the underwriters at the time of the
public offering. The Bank further agrees that the Company may impose stop
transfer instructions in order to enforce the foregoing covenants.

     IN WITNESS WHEREOF, the Company has caused this Warrant to be executed by
its officers thereunto duly authorized.

Dated: February 28, 2000.




                                  ClearCommerce Corporation


                                  By: /s/ Michael S. Grajeda
                                     ------------------------------------------
                                     Michael S. Grajeda, Vice President and
                                     Chief Financial Officer

                                       5
<PAGE>

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


TO:     ClearCommerce Corporation
        11500 Metric Blvd., Suite 300
        Austin, Texas  78758
        ATTN:  Secretary

     1. The undersigned hereby elects to purchase ______________ shares of the
_________________ (the "Shares") of ClearCommerce Corporation pursuant to the
                       --------
terms of the attached Warrant, and tenders herewith payment of the purchase
price in full, together with all applicable transfer taxes, if any.

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


               -------------------------------------------------
                                  (Print Name)
               Address:
                        ----------------------------------------

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

     3. The undersigned confirms that the Shares are being acquired for the
account of the undersigned for investment only 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 selling the Shares.


------------------------------------      --------------------------------------
(Date)                                    (Signature)

                                          --------------------------------------
                                          (Print Name)
<PAGE>

                              NOTICE OF CONVERSION
                              --------------------

TO:     ClearCommerce Corporation
        11500 Metric Blvd., Suite 300
        Austin, Texas  78758
        ATTN:  Secretary

     1. The undersigned hereby elects to convert the attached Warrant into such
number of shares of _________________ ClearCommerce Corporation (the "Shares")
                                                                     --------
as is determined pursuant to Section 2 of such Warrant, which conversion shall
be effected pursuant to the terms of the attached Warrant.

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



               -------------------------------------------------
                                  (Print Name)
               Address:
                        ----------------------------------------

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


     3. The undersigned represents that the Shares 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.




------------------------------------      --------------------------------------
(Date)                                    (Signature)

                                          --------------------------------------
                                          (Print Name)