Paul Byrd (10-11) got his third consecutive win after allowing four runs on seven hits and a walk in seven innings. Three of the four runs came on solo home runs.
Jason Varitek and Jeff Bailey had solo homers for Boston. Jed Lowrie had a double, two RBI and three walks.
Pedroia's two hits gave him 185 this season, which set a Red Sox franchise record for hits in a season among second basemen.
Baltimore starter Garrett Olson (8-7) was recalled from Triple-A Norfolk in time for Monday's game and was charged with the loss after allowing six runs on six hits and five walks in 5 2/3 innings.
Adam Jones, activated from the 15-day disabled list Monday, had one of the Orioles' three solo homers. Juan Castro and Kevin Millar had the others for Baltimore, which has lost nine of 10 games.