Josh Rutledge filled in at second base.
Pedroia has performed well since his return from the disabled list on Sept. 8, hitting .320 with three homers and eight RBIs.
David Ortiz also got the night off after belting homer No. 37 on Friday. The slugger has had general soreness that has limited his playing time over the final week of the season. Interim manager Torey Lovullo didn't rule Ortiz out for the season finale on Sunday.
Don't look for catcher Ryan Hanigan to play again this season.