He fouled a pitch off his in-step in the top of the fourth of New York's 9-6, 12-inning victory against the Twins Tuesday night.
Despite the injury, the 14-year veteran stayed in the contest, compiling three hits and one RBI before he was lifted for a pinch-runner in the ninth.
"He's sore," Yankees manager Joe Girardi said on the Yankees' Web site before Wednesday's contest. "He's available to pinch-hit (but) I just didn't think he was well enough to play nine innings. I thought about using him as the designated hitter, but we're not there."
Jeter had X-rays taken at a Minneapolis hospital, and they were negative.
He did not speak to reporters before Wednesday's game, receiving treatment in the trainers' room.
Jeter is hitting .284 with seven home runs and 57 RBIs in 113 games (454 at-bats) this season.