Jeter said he felt fine, but manager Joe Girardi wanted to give him and Alex Rodriguez a chance to rest by keeping them both out of the starting lineup.
Rodriguez later entered the game as a pinch runner when Eric Chavez came up injured. The Tigers beat the Yankees on Thursday, 6-3.
Jeter left during the eighth inning Wednesday night. He said afterward it was nothing serious, but Girardi described him as day-to-day.
"It isn't an injury. I have had zero treatment. I wish I had something to tell you. I had no idea I wasn't in the lineup until I walked in and didn't see my name," Jeter said. "I'm not happy about it. I always want to play. But I'm not upset."
Before Thursday's game against the Tigers, Girardi said he would have given Jeter a day off regardless -- although he said Jeter didn't look 100 percent the previous night.
"I saw him run yesterday when he ran to first. To me, it looked like it was bothering him a little bit," Girardi said. "He was going to get a day off at some point during this long stretch, so I chose today."
Girardi indicated there's no reason Jeter shouldn't be able to play Friday night at Texas.
Chavez replaced A-Rod at third base, but he left the game after appearing to hurt his left foot while hitting an RBI triple in the fourth inning. Rodriguez entered as a pinch-runner and stayed in the game, his first pinch-running appearance since 1995, according to STATS LLC.
"You are looking at 145 to 150 (games) over the course of the year," the 35-year-old Rodriguez said. "I think Joe is going to be very smart with my games played."
Rodriguez last pinch-ran for Seattle in the decisive fifth game of the American League Division Series against the Yankees and scored the tying run in the eighth inning. The Mariners went on to win in 11.
The 36-year-old Jeter is off to a quiet start, hitting .250 with only two extra-base hits. The Yankees are in the middle of a stretch of 16 games without an off day.
"I have to be smart about it. You can't play him every day when you're playing in 16 games in a row," Girardi said. "You just can't do it. I think the fresher our players are, the more productive they're going to be."
Girardi said he'd spoken with Rodriguez about the decision not to start him.
"I talked to Alex," he said. "I made the assumption that Derek might know."