Brett Gardner batted leadoff in Jeter's place.
Manager Joe Girardi said it had nothing to do with Jeter's recent struggles or the two double plays he hit into Monday night, including one in the ninth inning with the bases loaded that ended a burgeoning Yankee rally.
Girardi said that with Alex Rodriguez not playing due to a calf injury, he needed to move usual No. 2 hitter Nick Swisher to the middle of the order to protect Robinson Cano, who moved up to bat cleanup.
He also deflected questions about Jeter's performance this season, in which he is batting .278 -- 37 points below his career average and 66 points below the .334 he hit in 2009.
"Sometimes people think only about your last at-bat, but his August has been pretty good,'' Girardi said. "He has not had the same season that he had last year, but I haven't seen anything dramatic to say there's a reason why. He just hasn't quite had the season he's had last year.''
Jeter has shown a penchant for hitting the ball on the ground this season. About two-thirds of Jeter's contacts this year have been grounders -- the highest percentage in baseball -- and he has hit into 17 double plays so far, one behind his total for all of 2009.
"That's just means he's hitting the ball hard on the grounder with runners on base,'' Girardi said.
Tuesday marked the fourth time this season Jeter started in the No. 2 hole and the seventh time Gardner has batted leadoff. The new alignment paid dividends immediately when Gardner led off the first inning with a single, followed by a walk to Jeter. Both men scored later in the inning on a single by Swisher to give the Yankees a 2-1 lead.