Stewart was seen by Girardi and head athletic trainer Steve Donohue after reaching the bag and stayed in the game for one more batter, but he was replaced by Austin Romine behind the plate when the eighth inning started.
"When he went around the base and stopped, he said he felt something," Girardi said. "He said it didn't pop. He said he was OK, but when we saw him run, he said it continued to hurt."
Stewart has been assuming the bulk of the Yankees' catching duties since Francisco Cervelli went on the disabled list in late April with a fractured right hand. Stewart is hitting .265 with three homers and six RBIs in 24 games.
Girardi said that it was too soon to know if the Yankees would place Stewart on the disabled list, but it seems likely that journeyman Bobby Wilson would be first in line for a callup from Triple-A Scranton/Wilkes-Barre.
"You've got to move forward. That's the bottom line," Girardi said. "Injuries are a part of the game, and some years you're going to have more than others. Right now, we have a few and we have to move on. There's no excuses. You have to find a way to get it done."
Bryan Hoch is a reporter for MLB.com. Follow him on Twitter @bryanhoch and read his MLBlog, Bombers Beat. This story was not subject to the approval of Major League Baseball or its clubs.