The 6-foot-6 inch right-hander has been on the 15-day disabled list for most of the season with elbow discomfort caused by bone spurs.
He started for the reigning World Series champions on Opening Night April 1 against the New York Mets.
The 2005 Cy Young Award winner encountered elbow stiffness last Tuesday while throwing three simulated innings.
After that side session, team doctors decided the surgery was necessary.
"That's a huge hit," said Manager Tony La Russa on the team's Web site when told that Carpenter is expected to be sidelined for at least three more months. "That's part of the game, part of baseball. Our goal is to be in contention when he gets back."
"Hopefully, we can go in and get it done and my recovery will be faster than everybody hopes," Carpenter said.