Boston scored four runs in the eighth inning and two in the ninth to take the lead in a game that was delayed 59 minutes by a cold, late-spring rain.
Daniel Baird (1-1) got the win in relief of Josh Beckett, who gave up five runs -- three earned -- on five hits, three walks and six strikeouts.
Beckett lasted 4 2/3 innings before departing with what was reported to be back injury. The Yankees filed a protest with the umpires, contending there had been no indication Beckett was hurt. The reported injury allowed Manny Delcarmen to take extra time to warm up on the chilly night.
"They signaled to the bullpen before they announced to the bullpen that he was hurt," Yankees Manager Joe Girardi said. "You can't do that."
Mariano Rivera (0-1) took the loss with a rare clunker appearance in which he surrendered two runs on two hits in one inning.