Jeter suffered a bruised left instep in New York's 9-6, 12-inning victory on Tuesday, fouling a ball off his foot in the fourth inning against Twins right-hander Nick Blackburn.
Jeter was hobbled for a few moments but remained in the game and stroked three singles, including an RBI, before he was lifted for a pinch-runner in the ninth inning.
"He's sore," Yankees manager Joe Girardi said. "He's available to pinch-hit. I just didn't think he was well enough to play nine innings. I thought about DH-ing him, 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.
The 34-year-old All-Star is batting .284 with seven home runs and 57 RBIs in 113 games for New York this season. The Yankees have an off-day Thursday before opening a three-game weekend series in New York against the Royals on Friday.
"I'd be shocked if he didn't play Friday," Girardi said. "If we didn't have [Thursday] off, he still wouldn't have played today. What it allows us is an extra day to heal."
Wilson Betemit made the start at shortstop in place of Jeter.
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.