Exhibit 31.3 CERTIFICATIONS REQUIRED BY RULE 13 A-14(a) UNDER THE SECURITIES EXCHANGE ACT OF 1934 I, James S. Mahan, III, certify that: 1. I have reviewed this Annual Report on Form 10-K/A of S1 Corporation ("S1"); 2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report; 3. [Not applicable]; 4. [Not applicable]; and 5. [Not applicable]; Date: March 30, 2006 /S/ JAMES S. MAHAN, III - ----------------------------- James S. Mahan, III Chief Executive Officer