With both sides satisfied, Bonds is scheduled to report Monday to spring training. He is likely to participate in the Giants' first full-squad workout Tuesday.
"I expect he will be ready to go," general manager Brian Sabean said.
The 42-year-old Bonds is 22 homers shy of breaking Hank Aaron's career record of 755.
Bonds signed the contract Tuesday, and it was sent overnight mail to the Giants. The team then faxed a copy to the commissioner's office for approval.
His agent, Jeff Borris, and the Giants reached a preliminary agreement on Dec. 7, then spent weeks negotiating the final terms. The team announced the deal Jan. 29 and Bonds did an interview via conference call.
But his first contract contained a provision detailing his responsibilities for promotional appearances and was rejected by the commissioner's office. Management and the players' association agreed last year during bargaining not to allow any language in new contracts regarding promotional appearances other than the standard clause in all player contracts.
The deal also contained a provision stating the Giants could terminate the deal in the event Bonds is indicted, language Borris has said is unenforceable under baseball's labor agreement. A federal grand jury is investigating whether Bonds perjured himself when he testified in 2003 in the Bay Area Laboratory Co-Operative steroid distribution case that he hadn't knowingly taken any performance-enhancing drugs.
Bonds long has denied knowingly using steroids.
After the first contract was rejected by the commissioner's office, the Giants sent revised documents to Borris, but Bonds held off signing the revamped contract. Only the personal-appearance provision was deleted from the final deal, two baseball officials said. They spoke on condition of anonymity because of the sensitivity of such details.
Bonds will fill the final spot on the team's 40-man roster, which had stood at 39 after catcher Mike Matheny went on the voluntary retirement list with a concussion.
The seven-time NL MVP has been working out all offseason at UCLA and appears as healthy as ever, according to the Giants, Bonds' trainer and his agent. He had arthroscopic surgery on his troublesome left elbow after the 2006 season.
After missing all but 14 games in 2005 following three operations on his right knee, Bonds batted .270 with 26 homers and 77 RBIs and drew 115 walks in 130 games last year.
Borris declined comment.
AP Baseball Writer Ronald Blum in Tampa, Fla., contributed to this report.