Assistant general manager David Forst said Chavez elected to have surgery now, rather than after the season, to increase his chances of being healthy in time for spring training.
"He's been dealing with this shoulder problem for a long time," Forst said. "Going in to repair the problem is his best chance now to open up next year feeling 100 percent."
An 11-year veteran and six-time Gold Glove award winner, Chavez batted .247 with two homers and 14 RBIs in 89 at-bats this season.
The surgery, tentatively scheduled for Wednesday, Aug. 13, will be performed by team orthopedist Dr. John Frazier.
Chavez, 30, had surgery to repair a torn labrum in his right shoulder last September, one of three operations he had during the offseason. He also had back surgery in October and left shoulder surgery in November.
"The good news is his back feels great and his left shoulder is not a problem," Forst said. "It seems like those two issues have been addressed. Going through an offseason last year and rehabbing three different surgeries at once was not easy. This time, he'll be able to focus on just one thing."
Chavez began this season on the disabled list while recovering from his back surgery, returning to the lineup on May 28. He was forced onto the disabled list July 2 because of inflammation in his right shoulder.
"Anytime you have a player of his caliber, you'd always love him to be in your lineup," manager Bob Geren said. "But looking at him getting this behind him and ready to contribute on a daily basis next year is exciting."
Oakland's first-round pick in the 1996 draft, Chavez was limited to 90 games last season because of back and shoulder pain.