The oft-injured Carpenter, the 2007 National League Cy Young Award winner, hurt himself in the fourth inning of Tuesday's 7-6 loss to Arizona while swinging a bat.
"I felt it a little bit in that swing and every warm-up pitch (in the fifth) got worse and worse," he said.
"No matter what happened in the game, the important thing is it looks like he is going to be out for a while," Manager Tony La Russa said on the team's Web site. "This is a (bad) day. I'm not going to fake it."
Carpenter underwent Tommy John surgery in the summer of 2007 because of an elbow problem, and in 2008, he tried to return late in the season before being sidelined with a shoulder ailment.