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                                                                   EXHIBIT 10.16


                          AGILE SOFTWARE CORPORATION

                        COMMON STOCK PURCHASE AGREEMENT

                                AUGUST 12, 1999
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                        COMMON STOCK PURCHASE AGREEMENT
                        -------------------------------

     THIS COMMON STOCK PURCHASE AGREEMENT (the "Agreement") is made as of the
16/th/ day of August, 1999, by and among Agile Software Corporation, a
California corporation (the "Company") and the investors listed on Schedule A
hereto (collectively, the "Investors" and individually, an "Investor"). Prior to
the consummation of this Agreement, the Company intends to reincorporate in the
State of Delaware and to assign all of its rights and obligations under this
Agreement to the Delaware corporation. All references to the Company herein are
deemed to include both the Company as a California corporation, and the Delaware
corporation subsequent to the reincorporation.

     THE PARTIES HEREBY AGREE AS FOLLOWS:

     1.   Purchase and Sale of Stock.
          --------------------------

          1.1  Sale and Issuance of Common Stock. Subject to the terms and
               ---------------------------------
conditions of this Agreement, each Investor agrees to purchase at the Closing,
and the Company agrees to sell and issue to each Investor at the Closing, that
number of shares of the Company's Common Stock (the "Common Stock") equal to the
quotient obtained by dividing the aggregate estimated purchase price set forth
opposite each Investor's name on Schedule A hereto by the Net Offering Price, as
                                 ----------
defined herein. The purchase price per share of Common Stock purchased by each
Investor (the "Net Offering Price") shall be the price per share paid by the
public in an initial public offering of the Company's Common Stock completed
prior to December 15, 1999, less the per share underwriting fees and discounts
paid by the Company in such initial public offering (but before the deduction of
offering expenses payable by the Company). No fractional shares shall be issued,
and the number of shares issuable to each Investor shall be rounded down to the
nearest 100 shares.

          1.2  Closing.  The purchase and sale of the Common Stock shall take
               -------
place at the offices of Gray Cary Ware & Freidenrich LLP, 400 Hamilton Avenue,
Palo Alto, California 94301-1825, at 10:00 A.M., on the date and at the time of
the closing of the Company's initial public offering, or at such other time and
place as the Company and the Investors purchasing a majority of the Common Stock
may mutually agree upon orally or in writing (which time and place are
designated as the "Closing"). At the Closing, the Company shall deliver to each
Investor a certificate representing the number of shares of Common Stock that
such Investor is purchasing against payment of the purchase price therefor by
check or wire transfer to an account specified by the Company.

     2.  Representations, Warranties and Covenants of the Company.  The Company
         --------------------------------------------------------
hereby represents, warrants and covenants to the Investors that, except as set
forth on a Schedule of Exceptions (the "Schedule of Exceptions") furnished to
the Investors, which exceptions shall be deemed to be representations and
warranties as if made hereunder:

          2.1  Organization, Good Standing and Qualification.  The Company is a
               ---------------------------------------------
corporation duly organized, validly existing and in good standing under the laws
of the State of California, and upon reincorporation will be duly organized,
validly existing and in good
<PAGE>

standing under the laws of the State of Delaware. The Company has all requisite
corporate power and authority to carry on its business as now conducted and as
currently proposed to be conducted. The Company is duly qualified to transact
business and is in good standing in each jurisdiction in which the failure to so
qualify would have a material adverse effect on its business or properties.

          2.2  Capitalization and Voting Rights.  The authorized capital of the
               --------------------------------
Company is as set forth in the Registration Statement on Form S-1 filed by the
Company with the Securities and Exchange Commission pursuant to the rules and
regulations of the Securities Act of 1933, as amended, a copy of which is
attached hereto as Exhibit A (such Registration Statement, as amended at the
                   ---------
time it becomes effective and including the information deemed to be a part of
the registration statement at the time of effectiveness, being hereinafter
referred to as the "Registration Statement").

          2.3  Subsidiaries.  The Company has such subsidiaries as disclosed in
               ------------
the Registration Statement, including the exhibits thereto.

          2.4  Authorization.  All corporate action on the part of the Company,
               -------------
its officers, directors and shareholders necessary for the authorization,
execution and delivery of this Agreement, the performance of all obligations of
the Company hereunder and thereunder, and the authorization, issuance (or
reservation for issuance), sale and delivery of the Common Stock being sold
hereunder has been taken or will be taken prior to the Closing, and this
Agreement constitutes valid and legally binding obligations of the Company,
enforceable in accordance with its terms, except (i) as limited by applicable
bankruptcy, insolvency, reorganization, moratorium and other laws of general
application affecting enforcement of creditors' rights generally, (ii) as
limited by laws relating to the availability of specific performance, injunctive
relief or other equitable remedies and (iii) to the extent the indemnification
provisions contained in this Agreement may be limited by applicable federal or
state securities laws.

          2.5  Valid Issuance of Common Stock.  The Common Stock that is being
               ------------------------------
purchased by the Investors hereunder, when issued, sold and delivered in
accordance with the terms of this Agreement for the consideration expressed
herein, will be duly and validly issued, fully paid and nonassessable, and will
be free of restrictions on transfer other than restrictions on transfer under
this Agreement and under applicable state and federal securities laws.

          2.6  Governmental Consents.  No consent, approval, order or
               ---------------------
authorization of, or registration, qualification, designation, declaration or
filing with, any federal, state or local governmental authority on the part of
the Company is required in connection with the consummation of the transactions
contemplated by this Agreement, except for any filings that may be required
pursuant to state or federal securities laws.

          2.7  Litigation.  There is no action, suit, proceeding or
               ----------
investigation pending or currently threatened against the Company that questions
the validity of this Agreement, or the right of the Company to enter into such
agreements, or to consummate the transactions contemplated hereby. The only
material litigation in which the Company is involved is described in the
Registration Statement.

                                       2
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          2.8  Patents and Trademarks.  The Company and its subsidiaries own or
               ----------------------
possess, or can acquire on reasonable terms, all material patents, patent
rights, licenses, inventions, copyrights, know-how (including trade secrets and
other unpatented or unpatentable proprietary or confidential information,
systems or procedures), trademarks, service marks and trade names currently
employed by them in connection with the business now operated by them, and
neither the Company nor any of its subsidiaries has received any notice of
infringement of or conflict with asserted rights of others with respect to any
of the foregoing which, singly or in the aggregate, if the subject of an
unfavorable decision, ruling or finding, would have a material adverse affect on
the Company and its subsidiaries, taken as a whole.

          2.9  Compliance with Other Instruments.  The Company is not in
               ---------------------------------
violation or default in any material respect of any provision of its Restated
Articles or Bylaws, or in any material respect of any instrument, judgment,
order, writ, decree or contract to which it is a party or by which it is bound,
or, to the best of its knowledge, of any provision of any federal or state
statute, rule or regulation applicable to the Company. The execution, delivery
and performance of this Agreement, and the consummation of the transactions
contemplated hereby and thereby will not result in any such violation or be in
conflict with or constitute, with or without the passage of time and giving of
notice, either a default under any such provision, instrument, judgment order,
writ, decree or contract or an event that results in the creation of any lien,
charge or encumbrance upon any assets of the Company or the suspension,
revocation, impairment, forfeiture or nonrenewal of any material permit,
license, authorization or approval applicable to the Company, its business or
operations or any of its assets or properties.

          2.10 Permits.  The Company has all franchises, permits, licenses and
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any similar authority necessary for the conduct of its business as now being
conducted by it, the lack of which could materially and adversely affect the
business, properties, prospects or financial condition of the Company, and the
Company believes it can obtain, without undue burden or expense, any similar
authority for the conduct of its business as currently planned to be conducted.
The Company is not in default in any material respect under any of such
franchises, permits, licenses or other similar authority.

          2.11 Disclosure.  The Company has provided the Investors with a copy
               ----------
of the Registration Statement as filed, and will provide the Investors with a
copy of any and all amendments to the Registration Statement filed by the
Company with the Securities and Exchange Commission prior to the Closing Date.
To the best of its knowledge, neither this Agreement nor any other statements or
certificates made or delivered in connection herewith or therewith contains any
untrue statement of a material fact or omits to state a material fact necessary
to make the statements herein or therein not misleading.

          2.12 Registrations Rights.  Except as provided in the Investors'
               --------------------
Rights Agreement, a copy of which is attached hereto as Exhibit B the Company
                                                        ---------
has not granted or agreed to grant any registration rights, including piggyback
rights, to any person or entity.

          2.13 Offering.  Subject to the accuracy of the Investors'
               --------
representations in Section 3 of this Agreement and in written responses to the
Company's inquiries, the offer, sale and issuance of the Common Stock to be
issued in conformity with the terms of this Agreement

                                       3
<PAGE>

constitutes transactions exempt from the registration requirements of Section 5
of the Securities Act.

     3.   Representations and Warranties-of the Investors.  Each Investor hereby
          -----------------------------------------------
represents and warrants that:

          3.1  Authorization.  The Investor has full power and authority to
               -------------
enter into this Agreement and such agreement constitutes its valid and legally
binding obligation, enforceable against such Investor in accordance with its
terms.

          3.2  Purchase Entirely for Own Account.  This Agreement is made with
               ---------------------------------
such Investor in reliance upon such Investor's representation to the Company,
which by such Investor's execution of this Agreement such Investor hereby
confirms, that the Common Stock to be received by such Investor (sometimes
referred to in this Section 3 as the "Securities") will be acquired for
investment for such Investor's own account, not as a nominee or agent, and not
with a view to the resale or distribution of any part thereof, and that such
Investor has no present intention of selling, granting any participation in or
otherwise distributing the same. By executing this Agreement, such Investor
further represents that such Investor does not have any contract, undertaking,
agreement or arrangement with any person to sell, transfer or grant
participations to such person or to any third person with respect to any of the
Securities.

          3.3  Disclosure of Information.  Such Investor believes it has
               -------------------------
received all the information it considers necessary or appropriate for deciding
whether to purchase the Common Stock. Such Investor further represents that it
has had an opportunity to ask questions and receive answers from the Company
regarding the terms and conditions of the offering of the Common Stock and the
business, properties, prospects and financial condition of the Company. The
foregoing, however, does not limit or modify the representations and warranties
of the Company in Section 2 of this Agreement or the right of each Investor to
rely thereon.

          3.4  Investment Experience.  Such Investor is an investor in
               ---------------------
securities of companies in the development stage and acknowledges that it is
able to fend for itself, can bear the economic risk of its investment, and has
such knowledge and experience in financial or business matters that it is
capable of evaluating the merits and risks of the investment in the Common
Stock. If other than an individual, such Investor also represents it has not
been organized for the purpose of acquiring the Common Stock.

          3.5  Accredited Investor.  Such Investor is an "accredited investor"
               ------------------
within the meaning of Securities and Exchange Commission ("SEC") Rule 501 of
Regulation D, as presently in effect.

          3.6  Restricted Securities.  Such Investor understands that the
               --------------------
Securities it is purchasing are characterized as "restricted securities" under
the federal securities laws inasmuch as they are being acquired from the Company
in a transaction not involving a public offering and that under such laws and
applicable regulations such securities may be resold without registration under
the Securities Act only in certain limited circumstances. In this connection,
such Investor represents that it is familiar with SEC Rule 144, as presently in
effect and understands the resale limitations imposed thereby and by the
Securities Act.

                                       4
<PAGE>

          3.7  Further Limitations on Disposition.  Without in any way limiting
               ----------------------------------
the representations set forth above, such Investor further agrees not to make
any disposition of all or any portion of the Securities unless and until the
transferee has agreed in writing for the benefit of the Company to be bound by
this Section 3, provided and to the extent this Section 3 is then applicable,
and:

               (a)  There is then in effect a Registration Statement under the
Securities Act covering such proposed disposition and such disposition is made
in accordance with such Registration Statement; or

               (b)  (i) Such Investor shall have notified the Company of the
proposed disposition and shall have furnished the Company with a detailed
statement of the circumstances surrounding the proposed disposition and (ii) if
reasonably requested by the Company, such Investor shall have furnished the
Company with an opinion of counsel, reasonably satisfactory to the Company, that
such disposition will not require registration of such shares under the
Securities Act.

               (c)  Notwithstanding the provisions of paragraphs (a) and (b)
above, no such registration statement or opinion of counsel shall be necessary
for a transfer by an Investor that is a partnership to a partner of such
partnership or a retired partner of such partnership who retires after the date
hereof, or to the estate of any such partner or retired partner or the transfer
by gift, will or intestate succession of any partner to his or her spouse or to
the siblings, lineal descendants or ancestors of such partner or his or her
spouse, if the transferee agrees in writing to be subject to the terms hereof to
the same extent as if he or she were an original Investor hereunder.

          3.8  Legends.  It is understood that the certificates evidencing the
               -------
Securities may bear one or all of the legends in substantially the form
specified below:

               (a)  "THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE
SECURITIES ACT OF 1933, AS AMENDED. THEY MAY NOT BE SOLD, OFFERED FOR SALE,
PLEDGED OR HYPOTHECATED IN THE ABSENCE OF A REGISTRATION STATEMENT IN EFFECT
WITH RESPECT TO THE SECURITIES UNDER SUCH ACT OR AN OPINION OF COUNSEL
SATISFACTORY TO THE COMPANY THAT SUCH REGISTRATION IS NOT REQUIRED OR UNLESS
SOLD PURSUANT TO RULE 144 OF SUCH ACT."

               (b)  Any legend required by the laws of the State of California,
including any legend required by the California Department of Corporations and
Sections 417 and 418 of the California Corporations Code.

     4.   Registration Rights.  The Company shall grant to each Investor piggy-
          -------------------
back registration rights only, pursuant to the same terms and conditions as is
set forth in Section 1.3 of the Fifth Amended and Restated Investors' Rights
Agreement dated as of June 4, 1998 by and between the Company and the investors
listed on schedule A thereto (the "Investors' Rights Agreement"), in the form
attached hereto as Exhibit B.
                   ---------

                                       5
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     5.   Conditions of Investors' Obligations at Closing.  The obligations of
          -----------------------------------------------
the Investors under subsection 1.1 of this Agreement are subject to the
fulfillment on or before the Closing of each of the following conditions :

          5.1  Representations and Warranties.  The representations and
               ------------------------------
warranties of the Company contained in Section 2 shall be true on and as of the
Closing with the same effect as though such representations and warranties had
been made on and as of the date of such Closing.

          5.2  Performance.  The Company shall have performed and complied with
               -----------
all agreements, obligations and conditions contained in this Agreement that are
required to be performed or complied with by it on or before the Closing.

          5.3  Compliance Certificate.  The President of the Company shall
               ----------------------
deliver to the Investors at the Closing a certificate stating that the
conditions specified in Sections 5.1 and 5.2 have been fulfilled and stating
that there shall have been no adverse change in the business, affairs,
operations, properties, assets or condition of the Company since the date of
this Agreement.

          5.4  Qualifications.  All authorizations, approvals or permits, if
               --------------
any, of any governmental authority or regulatory body of the United States or of
any state that are required in connection with the lawful issuance and sale of
the Securities pursuant to this Agreement shall be duly obtained and effective
as of the Closing.

          5.5  Effectiveness of the Registration Statement.  The Registration
               -------------------------------------------
Statement shall have been declared effective by the Securities and Exchange
Commission and the sale of the shares thereunder has been consummated.

     6.   Conditions of the Company's Obligations at Closing.  The obligations
          --------------------------------------------------
of the Company to the Investors under this Agreement are subject to the
fulfillment on or before the Closing of each of the following conditions by the
Investors, the waiver of which shall not be effective against the Company unless
in writing and signed on behalf of the Company:

          6.1  Representations and Warranties.  The representations and
               ------------------------------
warranties of each Investor contained in Section 3 shall be true on and as of
the Closing with the same effect as though such representations and warranties
had been made on and as of the Closing.

          6.2  Payment of Purchase Price.  Each Investor shall have delivered
               -------------------------
the purchase price specified in Section 1.1.

          6.3  Qualifications.  All authorizations, approvals or permits, if
               --------------
any, of any governmental authority or regulatory body of the United States or of
any state that are required in connection with the lawful issuance and sale of
the Securities pursuant to this Agreement shall be duly obtained and effective
as of the Closing.

          6.4  Waivers of Right of First Offer and Registration Rights.  Each
               -------------------------------------------------------
Major Investor (as defined in the Investors' Rights Agreement) shall have waived
(i) the right of first offer granted to such Investor thereunder and (ii) the
granting of registration rights to the Investors hereunder.

                                       6
<PAGE>

     7.  Termination.  Subject to the provisions of Section 7.4 below, this
         -----------
Agreement may be terminated at any time prior to the Closing Date as to any
Investor:

          7.1  by the mutual written agreement of the Investor and the Company;

          7.2  by the Company in its sole absolute discretion;

          7.3  by either the Company or the Investor if the initial public
offering of the Company's Common Stock has not been completed and consummated on
or prior to December 15, 1999.

          7.4  Any termination of this Agreement pursuant to Section 7.1, 7.2 or
7.3 shall be without further obligation or liability upon any party in favor of
any other party hereto.

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

          8.1  Survival of Warranties.  The warranties, representations and
               ----------------------
covenants of the Company and each Investor contained in or made pursuant to this
Agreement shall survive the execution and delivery of this Agreement and the
Closing for a period of two years.

          8.2  Successors and Assigns.  Except as otherwise provided herein, the
               ----------------------
terms and conditions of this Agreement shall inure to the benefit of and be
binding upon the respective successors and assigns of the parties (including
transferees of any Securities and including the successor to the Company upon
its reincorporation in Delaware). Nothing in this Agreement, express or implied,
is intended to confer upon any party other than the parties hereto or their
respective successors and assigns any rights, remedies, obligations or
liabilities under or by reason of this Agreement, except as expressly provided
in this Agreement.

          8.3  Governing Law.  This Agreement shall be governed by and construed
               -------------
under the laws of the State of California as applied to agreements among
California residents entered into and to be performed entirely within
California.

          8.4  Counterparts.  This Agreement may be executed in two or more
               ------------
counterparts, each of which shall be deemed an original, but all of which
together shall constitute one and the same instrument.

          8.5  Titles and Subtitles.  The titles and subtitles used in this
               --------------------
Agreement are used for convenience only and are not to be considered in
construing or interpreting this Agreement.

          8.6  Notices.  Unless otherwise provided, any notice required or
               -------
permitted under this Agreement shall be given in writing and shall be deemed
effectively given upon personal delivery to the party to be notified or upon
deposit with the United States Post Office, by registered or certified mail,
postage prepaid and addressed to the party to be notified at the address
indicated for such party on the signature page hereof, or at such other address
as such party may designate by ten days' advance written notice to the other
parties.

                                       7
<PAGE>

          8.7  Finder's Fee.  Each party represents that it neither is nor will
               ------------
be obligated for any finders' fee or commission in connection with this
transaction. Each Investor agrees to indemnify and to hold harmless the Company
from any liability for any commission or compensation in the nature of a
finders' fee (and the costs and expenses of defending against such liability or
asserted liability) for which such Investor or any of its officers, partners,
employees or representatives is responsible. The Company agrees to indemnify and
hold harmless each Investor from any liability for any commission or
compensation in the nature of a finders' fee (and the costs and expenses of
defending against such liability or asserted liability) for which the Company or
any of its officers, employees or representatives is responsible.

          8.8  Expenses.  Each party shall bear its own costs and expenses
               --------
incurred in connection with the negotiation, execution, delivery and performance
of this Agreement, including the costs and expenses of legal counsel.

          8.9  Amendments and Waivers.  Any term of this Agreement may be
               ----------------------
amended and the observance of any term of this Agreement may be waived (either
generally or in a particular instance and either retroactively or
prospectively), only with the written consent of the Company. Any amendment or
waiver effected in accordance with this paragraph shall be binding upon each
holder of any securities purchased under this Agreement at the time outstanding
(including securities into which such securities are convertible), each future
holder of all such securities and the Company.

          8.10 Severability.  If one or more provisions of this Agreement are
               ------------
held to be unenforceable under applicable law, such provision shall be excluded
from this Agreement and the balance of this Agreement shall be interpreted as if
such provision were so excluded and shall be enforceable in accordance with its
terms.

          8.11 Aggregation of Stock.  All shares of Common Stock held or
               --------------------
acquired by affiliated entities or persons shall be aggregated together for the
purpose of determining the availability of any rights under this Agreement.

          8.12 Arbitration.  Any disputes arising out of or related to this
               -----------
Agreement shall be resolved by final, binding arbitration in San Jose,
California pursuant to the commercial arbitration rules of the American
Arbitration Association ("AAA"). A single arbitrator shall be appointed pursuant
to the AAA rules within thirty (30) days of submission of the dispute to the
AAA. The arbitrator shall conduct the arbitration in accordance with the
commercial arbitration rules of the AAA then in effect. Any judgment upon the
award rendered by the arbitrator may be entered in any court having jurisdiction
over the subject matter thereof. The arbitrator shall have the authority to
grant any equitable and legal remedies that would be available in any judicial
proceeding instituted to resolve such dispute. Each party shall pay its own
costs and attorneys' fees, and the parties shall share the cost of the
arbitration (including the arbitrator's fee) equally. Notwithstanding the
foregoing, the parties irrevocably submit to the non-exclusive jurisdiction of
the Superior Court of the State of California, Santa Clara County, and the
United States District Court for the Northern District of California, San Jose
Branch, in any action to enforce an arbitration award.

                                       8
<PAGE>

          8.13  Entire Agreement.  This Agreement, the exhibits hereto and the
                ----------------
documents referred to herein constitute the entire agreement among the parties
and no party shall be liable or bound to any other party in any manner by any
warranties, representations or covenants, except as specifically set forth
herein or therein.

          8.14  Disclosure.  The Investors hereby acknowledge and agree that the
                ----------
Company shall be entitled to disclose the existence and terms of this Agreement
in any registration statement, prospectus, report or other document filed by the
Company pursuant to any state or federal securities laws or other applicable
laws.

                                       9
<PAGE>

     IN WITNESS WHEREOF, the parties have executed this Agreement as of the date
first above written.


                              AGILE SOFTWARE CORPORATION


                              By: /s/ Bryan D. Stolle
                                  --------------------------------------
                                  Bryan D. Stolle
                                  President and Chief Executive Officer

                              Address:  One Almaden Boulevard, 12th Floor San
                                        Jose, California 95113


              [SIGNATURE PAGE TO COMMON STOCK PURCHASE AGREEMENT]

                                       10
<PAGE>

     IN WITNESS WHEREOF, the parties have executed this Agreement as of the date
first above written.


"Investor"


_________________________________
Print name of Investor

By: /s/
    -----------------------------

Title:___________________________

Address:_________________________

_________________________________

_________________________________


              [SIGNATURE PAGE TO COMMON STOCK PURCHASE AGREEMENT]

                                       11
<PAGE>

                                  SCHEDULE A
                                  ----------


Investor Name                                        Aggregate Investment
-------------                                        --------------------
Dell USA, LP, a Texas Limited Partnership       $4,999,992.50  (256,016 shares)
Flextronics International, Ltd.                 $4,999,992.50  (256,016 shares)
                                              ----------------------------------
                                                $9,999,985.00  (512,032 shares)
                                              ----------------------------------

                                       12