Stubbs felt pain under his ribs and near his back after fouling off a pitch in the seventh inning. He eventually struck out in the at-bat but went back to his defensive position in the eighth.
He was replaced defensively in the ninth by Wilson Valdez.
Chris Heisey started in center field on Wednesday against the Pirates.
"We're hoping it's just a couple of days, but you have to be real careful with these things," said manager Dusty Baker. "It's in the oblique area, but it's not the oblique. If you end up tearing that thing, you can be out for a long time, and we can't afford that, with his defensive speed and the way he's been coming on lately. He's been swinging the bat better lately."
The Reds are 24-2 when Stubbs scores a run. Though he is hitting .235 overall, he has been productive out of the No. 2 spot in the batting order, hitting .280 with seven doubles, seven home runs, 17 RBIs and 12 stolen bases.