<PAGE>
 
                                                                   Exhibit 3.1


                          CERTIFICATE OF AMENDMENT
                                   OF THE
                            AMENDED AND RESTATED
                  CERTIFICATE OF INCORPORATION, AS AMENDED
                                     OF
                            SIEBEL SYSTEMS, INC.

        SIEBEL SYSTEMS, INC., a corporation organized and existing under and 
by virtue of the General Corporation Law of the State of Delaware, does hereby
certify:

        FIRST:  The name of the corporation is Siebel Systems, Inc. The 
corporation was originally incorporated under the name Siebel Acquisition 
Corporation.

        SECOND:  The date on which the Certificate of Incorporation of the 
corporation was filed with the Secretary of State of the State of Delaware was
May 9, 1996. An Amended and Restated Certificate of Incorporation of the 
corporation was filed with the Secretary of State of the State of Delaware on 
July 9, 1996. A Certificate of Amendment to the Amended and Restated 
Certificate of Incorporation was filed with the Secretary of State of the 
State of Delaware on December 2, 1996.

        THIRD:  The Board of Directors of the corporation, acting in 
accordance with the provisions of Section 242 of the General Corporation Law 
of the State of Delaware, adopted resolutions to amend the Amended and 
Restated Certificate of Incorporation of the corporation by deleting the first
paragraph of Article IV and substituting therefor a new first paragraph of 
Article IV in the following form:

                "This corporation is authorized to issue two classes of stock 
to be designated, respectively, "Common Stock" and "Preferred Stock." The 
total number of shares which the corporation is authorized to issue is three 
hundred two million (302,000,000) shares. Three hundred million (300,000,000) 
shares shall be Common Stock, each having a par value of one-tenth of one cent
($.001). Two million (2,000,000) shares shall be Preferred Stock, each having 
a par value of one-tenth of one cent ($.001)."

        FOURTH:  Thereafter, pursuant to a resolution of the Board of 
Directors, this Certificate of Amendment was submitted to the stockholders of 
the corporation for their approval and was duly adopted in accordance with the
provision of Section 242 of the General Corporation Law of the State of 
Delaware.

        IN WITNESS WHEREOF, Siebel Systems, Inc. has caused this Certificate 
of Amendment to be signed by its Chairman and Executive Officer and attested 
to by its Secretary this 27th day of February, 1998.
                         ----

                                SIEBEL SYSTEMS, INC.

                                /s/ Thomas M. Siebel
                                ----------------------------------------
                                Thomas M. Siebel
                                Chairman and Chief Executive Officer

        ATTEST:


        /s/ James C. Gaither
        ------------------------------
        James C. Gaither
        Secretary

<PAGE>
 
                            CERTIFICATE OF AMENDMENT
                                     OF THE
                              AMENDED AND RESTATED
                          CERTIFICATE OF INCORPORATION
                                       OF
                              SIEBEL SYSTEMS, INC.


          SIEBEL SYSTEMS, INC., a corporation organized and existing under and
by virtue of the General Corporation Law of the State of Delaware, does hereby
certify:

          FIRST:  The name of the corporation is Siebel Systems, Inc.  The
corporation was originally incorporated under the name Siebel Acquisition
Corporation.

          SECOND:  The date on which the Certificate of Incorporation of the
corporation was filed with the Secretary of State of the State of Delaware was
May 9, 1996.  An Amended and Restated Certificate of Incorporation of the
corporation was filed with the Secretary of State of the State of Delaware on
July 9, 1996.

          THIRD:  The Board of Directors of the corporation, acting in
accordance with the provisions of Section 242 of the General Corporation Law of
the State of Delaware, adopted resolutions to amend the Amended and Restated
Certificate of Incorporation of the corporation by deleting the first paragraph
of Article IV and substituting therefor a new first paragraph of Article IV in
the following form:

          "This corporation is authorized to issue two classes of stock
          to be designated, respectively, "Common Stock" and "Preferred
          Stock." The total number of shares which the corporation is
          authorized to issue is one hundred two million (102,000,00)
          shares. One hundred million (100,000,000) shares shall be
          Common Stock, each having a par value of one-tenth of one cent
          ($.001). Two million (2,000,000) shares shall be Preferred
          Stock, each having a par value of one-tenth of one cent ($.001)."

          FOURTH:  Thereafter, pursuant to a resolution of the Board of
Directors, this Certificate of Amendment was submitted to the stockholders of
the corporation for their approval and was duly adopted in accordance with the
provision of Section 242 of the General Corporation Law of the State of
Delaware.

          IN WITNESS WHEREOF,  Siebel Systems, Inc. has caused this Certificate
of Amendment to be signed by its Chairman and Chief Executive Officer and
attested to by its Secretary this 2nd day of December, 1996.

                                    SIEBEL SYSTEMS, INC.

                                    /s/ Thomas M. Siebel
                                    ------------------------------------
                                    Thomas M. Siebel
                                    Chairman and Chief Executive Officer

ATTEST:


/s/ James C. Gaither
--------------------
James C. Gaither
Secretary

<PAGE>
 
                              AMENDED AND RESTATED
                          CERTIFICATE OF INCORPORATION
                                       OF
                              SIEBEL SYSTEMS, INC.

          SIEBEL SYSTEMS, INC., a corporation organized and existing under the
laws of the state of Delaware (the "Corporation") hereby certifies that:

1.        The name of the Corporation is Siebel Systems, Inc..  The corporation
was originally incorporated under the name Siebel Acquisition Corporation.

2.        The date of filing of the Corporation's original Certificate of
Incorporation was May 9, 1996.

3.        The Amended and Restated Certificate of Incorporation of the
Corporation as provided in Exhibit A hereto was duly adopted in accordance with
the provisions of Section 242 and Section 245 of the General Corporation Law of
the State of Delaware by the Board of Directors of the corporation.

4.        Pursuant to Section 245 of the Delaware General Corporation Law,
approval of the stockholders of the corporation has been obtained.

5.        The Amended and Restated Certificate of Incorporation so adopted reads
in full as set forth in Exhibit A attached hereto and is hereby incorporated by
reference.

          IN WITNESS WHEREOF, the undersigned have signed this certificate this
3rd day of July, 1996, and  hereby affirm and acknowledge under penalty of
perjury that the filing of this Restated Certificate of Incorporation is the act
and deed of Siebel Systems, Inc.

                                    SIEBEL SYSTEMS, INC.


                                    By  /s/ Thomas M. Siebel
                                        __________________________          
                                        Thomas M. Siebel
                                        President and Chief Executive
                                        Officer

ATTEST:


/s/ Eric C. Jensen
________________________         
Eric C. Jensen
Assistant Secretary

                                       2.

<PAGE>
 
                              AMENDED AND RESTATED
                          CERTIFICATE OF INCORPORATION
                                       OF
                              SIEBEL SYSTEMS, INC.


                                       I.

          The name of this corporation is Siebel Systems, Inc.

                                      II.

          The address, including street, number, city and county of the
registered officer of the corporation in the State of Delaware is 1013 Centre
Road, City of Wilmington 19805, County of New Castle; and the name of the
registered agent of the corporation in the State of Delaware at such address is
The Prentice-Hall Corporation System, Inc.

                                      III.

          The purpose of this corporation is to engage in any lawful act or
activity for which a corporation may be organized under the General Corporation
Law of the State of Delaware.

                                      IV.

          This corporation is authorized to issue two classes of stock to be
designated, respectively, "Common Stock" and "Preferred Stock."  The total
number of shares which the corporation is authorized to issue is Forty-Two
Million (42,000,000) shares.  Forty Million (40,000,000) shares shall be Common
Stock, each having a par value of one tenth of one cent ($.001).  Two Million
(2,000,000) shares shall be Preferred Stock, each having a par value of one
tenth of one cent ($.001).

          The Preferred Stock may be issued from time to time in one or more
series.  The Board of Directors is hereby authorized, by filing a certificate (a
"Preferred Stock Designation") pursuant to the Delaware General Corporation Law,
to fix or alter from time to time the designation, powers, preferences and
rights of the shares of each such series and the qualifications, limitations or
restrictions of any wholly unissued series of Preferred Stock, and to establish
from time to time the number of shares constituting any such series or any of
them; and to increase or decrease the number of shares of any series subsequent
to the issuance of shares of that series, but not below the number of shares of
such series then outstanding.  In case the number of shares of any series shall
be decreased in accordance with the foregoing sentence, the shares constituting
such decrease shall resume the status that they had prior to the adoption of the
resolution originally fixing the number of shares of such series.

                                      3.

<PAGE>
 
 
                                       V.

          For the management of the business and for the conduct of the affairs
of the corporation, and in further definition, limitation and regulation of the
powers of the corporation, of its directors and of its stockholders or any class
thereof, as the case may be, it is further provided that:

1.

          (1) The management of the business and the conduct of the affairs of
the corporation shall be vested in its Board of Directors.  The number of
directors which shall constitute the whole Board of Directors shall be fixed
exclusively by one or more resolutions adopted by the Board of Directors.

          (2) Notwithstanding the foregoing provisions of this Article, each
director shall serve until his successor is duly elected and qualified or until
his death, resignation or removal.  No decrease in the number of directors
constituting the Board of Directors shall shorten the term of any incumbent
director.

          Subject to the rights of the holders of any series of Preferred Stock
to elect additional directors under specified circumstances, following the date
on which the corporation is no longer subject to Section 2115 of the California
Corporations Code (the "Qualifying Record Date"), the directors shall be divided
into three classes designated as Class I, Class II and Class III, respectively.
Directors shall be assigned to each class in accordance with a resolution or
resolutions adopted by the Board of Directors.  At the first annual meeting of
stockholders following the Qualifying Record Date, the term of office of the
Class I directors shall expire and Class I directors shall be elected for a full
term of three years.  At the second annual meeting of stockholders following the
Qualifying Record Date, the term of office of the Class II directors shall
expire and Class II directors shall be elected for a full term of three years.
At the third annual meeting of stockholders following the Qualifying Record
Date, the term of office of the Class III directors shall expire and Class III
directors shall be elected for a full term of three years.  At each succeeding
annual meeting of stockholders, directors shall be elected for a full term of
three years to succeed the directors of the class whose terms expire at such
annual meeting.

          (3) Subject to the rights of the holders of any series of Preferred
Stock, the Board of Directors or any individual director may be removed from
office at any time with cause by the affirmative vote of the holders of a
majority of the voting power of all the then-outstanding shares of voting stock
of the corporation, entitled to vote at an election of directors (the "Voting
Stock").  Subject to the rights of the holders of any series of Preferred Stock
and as except as otherwise provided by law, no director of the Company may be
removed from office without cause.

          (4) Subject to the rights of the holders of any series of Preferred
Stock, any vacancies on the Board of Directors resulting from death,
resignation, disqualification, removal or other causes and any newly created
directorships resulting from any increase in the number of directors, shall,
unless (i) the Board of Directors determines by resolution that any such
vacancies or newly created directorships shall be filled by the stockholders, or
(ii) as otherwise provided by law, be filled only by the affirmative vote of a
majority of the directors then in office, even though less than a quorum of the
Board of Directors, and not by the stockholders.  Any director elected in
accordance with the preceding sentence shall hold office for the remainder of
the full term of the director for which the vacancy was created or occurred and
until such director's successor shall have been elected and qualified.

                                      4.

<PAGE>
 
2.
          (a) Subject to paragraph (h) of Section 43 of the Bylaws, following
the closing of the initial public offering pursuant to an effective registration
statement under the Securities Act of 1933, as amended, covering the offer and
sale of Common Stock to the public (the "Initial Public Offering"), the Bylaws
may be altered or amended or new Bylaws adopted by the affirmative vote of at
least sixty-six and two-thirds percent (66-2/3%) of the voting power of all of
the then-outstanding shares of the Voting Stock.  The Board of Directors shall
also have the power to adopt, amend, or repeal Bylaws.

          (b) The directors of the corporation need not be elected by written
ballot unless the Bylaws so provide.
          
          (c) No action shall be taken by the stockholders of the corporation
except at an annual or special meeting of stockholders called in accordance with
the Bylaws and following the closing of the Initial Public Offering no action
shall be taken by the stockholders by written consent.
          
          (d) Special meetings of the stockholders of the corporation may be
called, for any purpose or purposes, by (i) the Chairman of the Board of
Directors, (ii) the Chief Executive Officer or (iii) the Board of Directors
pursuant to a resolution adopted by a majority of the total number of authorized
directors (whether or not there exist any vacancies in previously authorized
directorships at the time any such resolution is presented to the Board of
Directors for adoption).
          
          (e) Advance notice of stockholder nominations for the election of
directors and of business to be brought by stockholders before any meeting of
the stockholders of the corporation shall be given in the manner provided in the
Bylaws of the corporation.

                                      VI.

1.        A director of the corporation shall not be personally liable to the
corporation or its stockholders for monetary damages for any breach of fiduciary
duty as a director, except for liability (i) for any breach of the director's
duty of loyalty to the corporation or its stockholders, (ii) for acts or
omissions not in good faith or which involve intentional misconduct or a knowing
violation of law, (iii) under Section 174 of the Delaware General Corporation
Law, or (iv) for any transaction from which the director derived an improper
personal benefit.  If the Delaware General Corporation Law is amended after
approval by the stockholders of this Article to authorize corporate action
further eliminating or limiting the personal liability of directors, then the
liability of a director shall be eliminated or limited to the fullest extent
permitted by the Delaware General corporation Law, as so amended.

2.        Any repeal or modification of this Article VI shall be prospective and
shall not affect the rights under this Article VI in effect at the time of the
alleged occurrence of any act or omission to act giving rise to liability or
indemnification.

                                      VII.

1.        The corporation reserves the right to amend, alter, change or repeal
any provision contained in this Certificate of Incorporation, in the manner now
or hereafter prescribed by statute, except as provided in paragraph 2. of this
Article VII, and all rights conferred upon the stockholders herein are granted
subject to this reservation.

                                      5.

<PAGE>
 
2.        Notwithstanding any other provisions of this Certificate of
Incorporation or any provision of law which might otherwise permit a lesser vote
or no vote, but in addition to any affirmative vote of the holders of any
particular class or series of the Voting Stock required by law, this Certificate
of Incorporation or any Preferred Stock Designation, following the Initial
Public Offering the affirmative vote of the holders of at least sixty-six and
two-thirds percent (66 2/3%) of the voting power of all of the then outstanding
shares of the Voting Stock, voting together as a single class, shall be required
to alter, amend or repeal Articles V, VI and VII (other than any amendment of
such Articles in connection with a restatement of the Certificate of
Incorporation).

                                      6.