"We're just giving him an off day," Yankees manager Joe Girardi said. "There's nothing physical."
Rookie Eduardo Nuñez started at shortstop against Toronto.
Jeter entered Friday's game hitting just .266, nearly 50 points below his career average.
He has just three hits in his past 34 at-bats.
"He's just having not a Derek Jeter year," said Girardi, who noted that the captain's mechanics at the plate may be off. "He's been pretty productive. His average just isn't as high as normal."
Jeter has played 132 of the Yankees' 135 games this season, including 125 at shortstop. Girardi suggested that he's been forced to play Jeter more, with Alex Rodriguez (calf) on the disabled list.
"Maybe that has a little something to do with [Jeter's struggles]," the manager said.
Girardi pointed out that Jeter still has scored 95 runs and driven in 59 this year.
"Most people would write that in from their leadoff hitter," Girardi said.
Ian Begley is a regular contributor to ESPNNewYork.com.