Yankees manager Joe Girardi reiterated that nothing was bothering Jeter; he just wanted to give the captain some rest, and the shortstop confirmed he's fine.
"Just a day off," Girardi said. "We're in the midst of 16 [games] in a row. You give him today, maybe he can play the rest of the way out, maybe play some DH somewhere against Kansas City.
"At some point, I had to do it. He hasn't had a day off all year."
New York will return home after its mini two-game set in Toronto. After a three-game weekend series versus the Reds, the club will host the Royals.
Jeter, who is batting a team-best .366 while leading the Yankees with a .936 on-base plus slugging percentage, entered Wednesday's contest tied for the most multihit games in the Majors (17) after playing in each of the Yankees' first 36 games.
Granderson, meanwhile, led off for the first time this season. He has spent the majority of the year batting out the two-hole and has also seen some time in the No. 6 spot.
"That's the next guy if Jeter is not going to be in the lineup," Girardi said of Granderson. "I'm comfortable putting him there."
Granderson entered the game with a .273 average in 2,540 career plate appearances as a leadoff hitter. The center fielder had just four at-bats out of the No. 1 spot since joining New York in 2010, however.
Granderson will continue to hit second in the lineup moving forward, despite the fact that since the start of last season, he has hit 54 home runs, the most in the Majors. Girardi was asked if he thought about moving the slugger to the middle of the order because of his power, but the manager wasn't keen on the idea.
"I probably have five guys that are capable of hitting 30 homers," Girardi said.
"It's a different lineup than it was 20 years ago, when you maybe had two guys."