<PAGE>

                                                                   EXHIBIT 10.21

                              Warrant Certificate



          NEITHER THESE WARRANTS NOR THE SHARES UNDERLYING THESE
          WARRANTS HAVE BEEN REGISTERED UNDER THE SECURITIES ACT OF
          1933 OR THE LAWS OF ANY STATE. THEY MAY NOT BE SOLD OR
          OTHERWISE TRANSFERRED UNLESS THEY ARE REGISTERED UNDER SUCH
          ACT AND APPLICABLE STATE SECURITIES LAWS OR AN EXEMPTION
          FROM REGISTRATION IS AVAILABLE. THESE WARRANTS AND THE
          SHARES UNDERLYING THESE WARRANTS ARE ALSO SUBJECT TO
          ADDITIONAL RESTRICTIONS ON TRANSFER SET FORTH IN THE
          PURCHASE AGREEMENT OF EVEN DATE HEREWITH, A COPY OF WHICH
          MAY BE OBTAINED FROM INTRALINKS INC.


                                                      2,700 Warrants

                                INTRALINKS INC.

                              WARRANT CERTIFICATE

          This warrant certificate ("Warrant Certificate") certifies that for
value received, Eugene A. Tomei or registered assigns (the "Holder") is the
owner of the number of warrants ("Warrants") specified above, each of which
entitles the Holder thereof to purchase, at any time on or before the Expiration
Date (hereinafter defined) one fully paid and non-assessable share of the Series
B Preferred Stock, par value $0.01 per share ("Series B Preferred Stock"), of
IntraLinks Inc., a Delaware corporation (the "Company"), at a purchase price per
share of Series B Preferred Stock as set forth herein in lawful money of the
United States of America in cash or by certified or cashier's check.

     1.   Warrant; Purchase Price
          -----------------------

          Each Warrant shall entitle the Holder initially to purchase one share
of Series B Preferred Stock of the Company and the purchase price per share of
Series B Preferred Stock payable upon exercise of the Warrants (the "Purchase
Price") shall initially be $6.50; provided, however, that in the event of an
adjustment to the conversion price of the Series B Preferred Stock pursuant to
the Series B Preferred Stock Certificate of Designation dated December 17, 1997,
as amended, the Purchase Price shall be similarly adjusted.  The Purchase Price
and number of shares of Series B Preferred Stock issuable upon exercise of each
Warrant are subject to adjustment as provided in Article 6.  The shares of
Series B Preferred Stock issuable upon exercise of the Warrants (and/or other
shares of Series B Preferred Stock so issuable by reason of any adjustments
pursuant to Article 6) are sometimes referred to herein as the "Warrant Shares."
<PAGE>

     2.   Exercise; Expiration Date
          -------------------------

          2.1  The Warrants are exercisable, at the option of the Holder, in
whole or in part at any time and from time to time after issuance and on or
before the Expiration Date, upon surrender of this Warrant Certificate to the
Company together with a duly completed Notice of Exercise, in the form attached
hereto as Exhibit A, and payment of an amount equal to the Purchase Price times
          ---------
the number of Warrants to be exercised.  In the case of exercise of less than
all the Warrants represented by this Warrant Certificate, the Company shall
cancel the Warrant Certificate upon the surrender thereof and shall execute and
deliver a new Warrant Certificate for the balance of such Warrants.

          2.2  The term "Expiration Date" shall mean 5:00 p.m. New York time
five (5) years from the date hereof, or if such day shall in the State of New
York be a holiday or a day on which banks are authorized to close, then 5:00
p.m. New York time the next following day which in the State of New York is not
a holiday or a day on which banks are authorized to close.

     3.   Registration and Transfer on Company Books
          ------------------------------------------

          3.1  The Company shall maintain books for the registration and
transfer of the Warrants and the registration and transfer of the Warrant
Shares.

          3.2  Prior to due presentment for registration of transfer of this
Warrant Certificate, or the Warrant Shares, the Company may deem and treat the
registered Holder as the absolute owner thereof.

          3.3  The Company shall register upon its books any permitted transfer
of a Warrant Certificate, upon surrender of same to the Company with a written
instrument of transfer duly executed by the registered Holder or by a duly
authorized attorney.  Upon any such registration of transfer, new Warrant
Certificate(s) shall be issued to the transferee(s) and the surrendered Warrant
Certificate shall be canceled by the Company.  A Warrant Certificate may also be
exchanged, at the option of the Holder, for new Warrant Certificates of
different denominations representing in the aggregate the number of Warrants
evidenced by the Warrant Certificate surrendered.

     4.   Reservation of Shares
          ---------------------

          The Company covenants that it will as promptly as practicable
following the date of this Warrant, reserve and keep available out of its
authorized capital stock, solely for the purpose of issue upon exercise of the
Warrants, such number of shares of Series B Preferred Stock as shall then be
issuable upon the exercise of all outstanding Warrants.  The Company covenants
that all shares of capital stock which shall be issuable upon exercise of the
Warrants shall, at the time of such exercise, be duly and validly issued and
fully paid and non-assessable and free from all taxes, liens and charges with
respect to the issue thereof, and that upon

                                      -2-
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issuance such shares shall be listed on each national securities exchange, if
any, on which the other shares of such outstanding capital stock of the Company
are then listed.

     5.   Loss or Mutilation
          ------------------

          Upon receipt by the Company of reasonable evidence of the ownership of
and the loss, theft, destruction or mutilation of any Warrant Certificate and,
in the case of loss, theft or destruction, of indemnity reasonably satisfactory
to the Company, or, in the case of mutilation, upon surrender and cancellation
of the mutilated Warrant Certificate, the Company shall execute and deliver in
lieu thereof a new Warrant Certificate representing an equal number of Warrants.

     6.   Adjustment of Purchase Price
          and Number of Shares Deliverable
          --------------------------------

          6.1  The number of Warrant Shares purchasable upon the exercise of
each Warrant and the Purchase Price with respect to the Warrant Shares shall be
subject to adjustment as follows:

               (a)  In case the Company shall (i) declare a dividend or make a
     distribution on its Series B Preferred Stock payable in shares of its
     capital stock, (ii) subdivide its outstanding shares of Series B Preferred
     Stock through stock split or otherwise, (iii) combine its outstanding
     shares of Series B Preferred Stock into a smaller number of shares of
     Series B Preferred Stock, or (iv) issue by reclassification of its Series B
     Preferred Stock (including any such reclassification in connection with a
     consolidation or merger in which the Company is the continuing corporation)
     other securities of the Company, the number and/or nature of Warrant Shares
     purchasable upon exercise of each Warrant immediately prior thereto shall
     be adjusted so that the Holder shall be entitled to receive the kind and
     number of Warrant Shares or other securities of the Company which he would
     have owned or have been entitled to receive after the happening of any of
     the events described above, had such Warrant been exercised immediately
     prior to the happening of such event or any record date with respect
     thereto.  An adjustment made pursuant to this paragraph (a) shall become
     effective retroactively as of the record date of such event.

               (b)  In the event of any capital reorganization or any
     reclassification of the capital stock of the Company or in case of the
     consolidation or merger of the Company with another corporation (other than
     a consolidation or merger in which the outstanding shares of the Company's
     Series B Preferred Stock are not converted into or exchanged for other
     rights or interests), or in the case of any sale, transfer or other
     disposition to another corporation of all or substantially all the
     properties and assets of the Company, the Holder of each Warrant shall
     thereafter be entitled to purchase (and it shall be a condition to the
     consummation of any such reorganization, reclassification, consolidation,
     merger, sale, transfer or other disposition that appropriate provisions
     shall be made so that such Holder shall thereafter be entitled to purchase)
     the kind and amount of shares

                                      -3-
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     of stock and other securities and property (including cash) which the
     Holder would have been entitled to receive had such Warrants been exercised
     immediately prior to the effective date of such reorganization,
     reclassification, consolidation, merger, sale, transfer or other
     disposition; and in any such case appropriate adjustments shall be made in
     the application of the provisions of this Article 6 with respect to rights
     and interest thereafter of the Holder of the Warrants to the end that the
     provisions of this Article 6 shall thereafter be applicable, as near as
     reasonably may be, in relation to any shares or other property thereafter
     purchasable upon the exercise of the Warrants. The provisions of this
     Section 6.1(b) shall similarly apply to successive reorganizations,
     reclassifications, consolidations, mergers, sales, transfers or other
     dispositions.

               (c)  Whenever the number of Warrant Shares purchasable upon the
     exercise of each Warrant is adjusted, as provided in this Section 6.1, the
     Purchase Price with respect to the Warrant Shares shall be adjusted by
     multiplying such Purchase Price immediately prior to such adjustment by a
     fraction, of which the numerator shall be the number of Warrant Shares
     purchasable upon the exercise of each Warrant immediately prior to such
     adjustment, and of which the denominator shall be the number of Warrant
     Shares so purchasable immediately thereafter.

          6.2  No adjustment in the number of Warrant Shares purchasable under
the Warrants, or in the Purchase Price with respect to the Warrant Shares, shall
be required unless such adjustment would require an increase or decrease of at
least 1% in the number of Warrant Shares issuable upon the exercise of such
Warrant, or in the Purchase Price thereof; provided, however, that any
adjustments which by reason of this Section 6.2 are not required to be made
shall be carried forward and taken into account in any subsequent adjustment.

          6.3  Whenever the number of Warrant Shares purchasable upon the
exercise of each Warrant or the Purchase Price of such Warrant Shares is
adjusted, as herein provided, the Company shall mail to the Holder, at the
address of the Holder shown on the books of the Company, a notice of such
adjustment or adjustments, prepared and signed by an officer of the Company,
which sets forth the number of Warrant Shares purchasable upon the exercise of
each Warrant and the Purchase Price of such Warrant Shares after such
adjustment, and a brief statement of the facts requiring such adjustment.

          6.4  The form of Warrant Certificate need not be changed because of
any change in the Purchase Price, the number of Warrant Shares issuable upon the
exercise of a Warrant or the number of Warrants outstanding pursuant to this
Section 6, and Warrant Certificates issued before or after such change may state
the same Purchase Price, the same number of Warrants, and the same number of
Warrant Shares issuable upon exercise of Warrants as are stated in the Warrant
Certificates theretofore issued pursuant to this Agreement.  The Company may,
however, at any time, in its sole discretion, make any change in the form of
Warrant Certificate that it may deem appropriate and that does not affect the
substance thereof, and any Warrant Certificates thereafter issued or
countersigned, whether in exchange

                                      -4-
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or substitution for an outstanding Warrant Certificate or otherwise, may be in
the form as so changed.

     7.   Conversion Rights.
          -----------------

          In lieu of exercising this Warrant or any portion hereof, the Holder
hereof shall have the right to convert this Warrant or any portion hereof into
Warrant Shares by executing and delivering to the Company at its principal
office the written Notice of Conversion attached hereto as Exhibit B, specifying
                                                           ---------
the portion of the Warrant Shares to be converted and accompanied by this
Warrant.  The number of Warrant Shares to be issued to Holder upon such
conversion shall be computed using the following formula:

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

where     X=   the number of Warrant Shares to be issued to the Holder for the
               portion of the Warrant being converted.

          P=   the portion of the Warrant being converted expressed as a decimal
               fraction.

          Y=   the total number of Warrant Shares issuable upon exercise of the
               Warrant in full.

          A=   the fair market value of one Warrant Share shall mean (i) the
               fair market value of one share of the Company's Series B
               Preferred Stock as of the last business day immediately prior to
               the date the notice of conversion is received by the Company, as
               determined in good faith by the Company's Board of Directors, or
               (ii) if this Warrant is being converted in conjunction with a
               public offering of the Company's common stock, par value $.01
               (the "Common Stock"), the price to the public per share of Common
               Stock pursuant to the offering.

          B=   the Purchase Price on the date of conversion.

Any portion of this Warrant that is converted shall be immediately canceled.
This Warrant or any portion hereof shall be deemed to have been converted
immediately prior to the close of business on the date of its surrender for
conversion as provided above, and the person entitled to receive the Warrant
Shares issuable upon such conversion shall be treated for all purposes as Holder
of such shares of record as of the close of business on such date.  As promptly
as practicable after such date, the Company shall issue and deliver to the
person or persons entitled to receive the same a certificate or certificates for
the number of full Warrant Shares issuable upon such conversion.  If the Warrant
shall be converted for less than the total number of Warrant Shares then
issuable upon conversion, promptly after surrender of the Warrant upon such
conversion, the Company will execute and deliver a new Warrant, dated the date
hereof,

                                      -5-
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evidencing the right of the Holder to the balance of the Warrant Shares
purchasable hereunder upon the same terms and conditions set forth herein.

     8.   Voluntary Adjustment by the Company
          -----------------------------------

          The Company may, at its option, at any time during the term of the
Warrants, reduce the then current Purchase Price to any amount deemed
appropriate by the Board of Directors of the Company and/or extend the date of
the expiration of the Warrants.

     9.   Fractional Shares and Warrants;
          Determination of Market Price Per Share
          ---------------------------------------

          9.1  Anything contained herein to the contrary notwithstanding, the
Company shall not be required to issue any fraction of a share of Series B
Preferred Stock in connection with the exercise of Warrants.  Warrants may not
be exercised in such number as would result (except for the provisions of this
paragraph) in the issuance of a fraction of a share of Series B Preferred Stock
unless the Holder is exercising all Warrants then owned by the Holder.  In such
event, the Company shall, upon the exercise of all of such Warrants, issue to
the Holder the largest aggregate whole number of shares of Series B Preferred
Stock called for thereby upon receipt of the Purchase Price for all of such
Warrants and pay a sum in cash equal to the remaining fraction of a share of
Series B Preferred Stock, multiplied by its Market Price Per Share (as
determined pursuant to Section 9.2 below) as of the last business day preceding
the date on which the Warrants are presented for exercise.

          9.2  As used herein, the "Market Price Per Share" with respect to any
share of stock on any specified date shall mean the closing price per share of
such stock for the trading day immediately preceding such date.  The closing
price for each such day shall be the last sale price regular way or, in case no
such sale takes place on such day, the average of the closing bid and asked
prices regular way, in either case on the principal securities exchange on which
the shares of such stock of the Company are listed or admitted to trading, the
last sale price, or in case no sale takes place on such day, the average of the
closing bid and asked prices of such stock on NASDAQ or any comparable system,
or if such stock is not reported on NASDAQ, or a comparable system, the average
of the closing bid and asked prices as furnished by two members of the National
Association of Securities Dealers, Inc. selected from time to time by the
Company for that purpose.  If such bid and asked prices are not available, then
"Market Price Per Share" shall be equal to the fair market value of such stock
as determined in good faith by the Board of Directors of the Company.

     10.  Restriction Upon Transfer; Securities Law Matters.
          -------------------------------------------------

THESE WARRANTS MAY NOT BE SOLD, TRANSFERRED OR OTHERWISE DISPOSED OF BY THE
HOLDER, EXCEPT AS SPECIFICALLY PROVIDED IN THE PURCHASE AGREEMENT OF EVEN DATE
HEREWITH BETWEEN THE COMPANY AND THE HOLDER.  THESE WARRANTS HAVE NOT BEEN
REGISTERED UNDER THE

                                      -6-
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SECURITIES ACT OF 1933, AS AMENDED, OR STATE SECURITIES LAWS AND MAY NOT BE
SOLD, ASSIGNED OR TRANSFERRED UNLESS SUCH SALE, ASSIGNMENT OR TRANSFER OF THESE
WARRANTS IS REGISTERED UNDER THE ACT AND APPLICABLE STATE SECURITIES LAWS OR
UNLESS AN EXEMPTION FROM REGISTRATION IS AVAILABLE.

     11.  Governing Law
          -------------

          This Warrant Certificate shall be governed by and construed in
accordance with the laws of the State of Delaware.

     12.  Issue Tax
          ---------

          The issuance of Warrant Shares upon exercise of the Warrants shall be
made without charge to the holders of such Warrants for any issuance tax in
respect thereof provided that the Company shall not be required to pay any tax
which may be payable in respect of any transfer involved in the issuance and
delivery of any certificate in a name other than that of any holder of the
Warrants.

     13.  Registration Rights
          -------------------

          The rights of the holder hereof with respect to registration under the
Securities Act of 1933, as amended, of the Warrant Shares are set forth in the
Registration Rights Agreement dated as of December 18, 1997 by and among the
Company and the several parties to such agreement.

                                      -7-
<PAGE>

     IN WITNESS WHEREOF, the Company has caused this Warrant Certificate to be
duly executed by its officers thereunto duly authorized and its corporate seal
to be affixed hereon, as of this 20/th/ day of August, 1998.


                                    INTRALINKS INC.



                                    By: /s/
                                        --------------------------------
                                        Name:
                                        Title:
<PAGE>

                                                                       EXHIBIT A


                              NOTICE OF EXERCISE


          The undersigned hereby irrevocably elects to exercise, pursuant to
Section 2 of the Warrant Certificate accompanying this Notice of Exercise,
_______ Warrants of the total number of Warrants owned by the undersigned
pursuant to the accompanying Warrant Certificate, and herewith makes payment of
the Purchase Price of such shares in full.



                                        ______________________________
                                        Name of Holder


                                        ______________________________
                                        Signature

                                        Address:

                                        ______________________________

                                        ______________________________

                                        ______________________________
<PAGE>

                                                                       EXHIBIT B


                             NOTICE OF CONVERSION


The undersigned hereby irrevocably elects to convert, pursuant to Section 7 of
the Warrant Certificate accompanying this Notice of Conversion, _______ Warrants
of the total number of Warrants owned by the undersigned pursuant to the
accompanying Warrant Certificate into shares of the Series B Preferred Stock of
the Company (the "Shares").

The number of Shares to be received by the undersigned shall be calculated in
accordance with the provisions of Section 7 of the accompanying Warrant
Certificate.



                                        ______________________________
                                        Name of Holder


                                        ______________________________
                                        Signature

                                        Address:

                                        ______________________________

                                        ______________________________