Andrew Lambo added an RBI in the deciding frame and Travis Ishikawa hit a solo homer for the Pirates.
Brandon Cumpton picked up the win after allowing three hits and one run over 4 2/3 relief innings. Wandy Rodriguez served up a run on four hits in his four- inning start.
Johnny Gomes and Xander Bogaerts drove in a run each for the Red Sox, while Dalier Hinojosa took the loss after allowing both runs in the eighth.
Jake Peavy tossed 4 2/3 innings and gave up four hits and one run while fanning five.