Managers Joe Girardi and John Farrell adjusted their lineups for Saturday afternoon's game at Yankee Stadium.
Girardi says he doesn't want to overuse the 39-year-old Jeter and risk injury.
This is Jeter's last season. Girardi says he understands some fans might be disappointed, but that he's doing what's best for the team.
"I wasn't hired to put on a farewell tour," Girardi said.
Pedroia had batted second for Boston all season. Farrell says Pedroia has been expanding his strike zone and overly aggressive.
Pedroia has not drawn a walk in 50 at-bats this season. No one in the majors has hit more without a walk.
Pedroia also hasn't homered. Farrell says batting leadoff could get Pedroia to focus more on just getting on base.