Brandon Moss hit a solo homer, and Pedroia had a double and two singles for the Red Sox, who were held to three runs despite winning two of three against Toronto earlier in the week. Boston had 13 hits on Friday and won for just the third time in nine games.
Tampa Bay, coming off its first winning April in club history (14-12), lost for only the second time in 10 games. The Rays swept the Red Sox in St. Petersburg, Fla. last weekend.
The start was delayed 2 hours, 27 minutes by rain. Only a couple thousand fans remained in Fenway Park when the game ended at 12:48 a.m.
Clay Buchholz (2-2) allowed one run, five hits, walked four and struck out six in 5 1/3 innings. Jonathan Papelbon, the fifth Boston pitcher, worked a perfect ninth.
Pedroia was 1-for-21 before his RBI double gave Boston a 1-0 lead against Rays starter Edwin Jackson (2-3).
Moss homered onto a small roof above a TV camera stand in center field to make it 2-0. Jacoby Ellsbury had an RBI single after Jason Varitek singled and Julio Lugo walked. Ellsbury stole second. Pedroia drove in both with a single, making it 4-0, and advanced to second on left fielder Carl Crawford's throw. David Ortiz lined an RBI single to center.
Jackson gave up six runs on nine hits in four-plus innings.
Crawford scored Tampa Bay's first run on Buchholz's fifth-inning wild pitch. Akinori Iwamura had a sacrifice fly and Crawford a run-scoring ground out in the seventh against reliever Javier Lopez.