"It's just a day off. That's the benefit of Holt. We can put him in a bunch of different positions," Farrell said. "It was [Pedroia's] day to be next to us on the bench."
The utility man came into Sunday's game riding a five-game hit streak and recording multiple hits in three of his four starts.
Pedroia went 0-for-4 with two strikeouts in Saturday's 4-1 loss to Baltimore and left five men on-base.
"Dustin's a guy who wants to play every day," Farrell said. "We've had a chance to talk over time to build in a periodic day off. Today is just one of those days."
Mookie Betts assumed Pedroia's spot in the two-hole, with Holt serving as the leadoff man.
Quinn Roberts is a reporter for MLB.com. Follow her on Twitter at @qlr5001. This story was not subject to the approval of Major League Baseball or its clubs.