Before the game, Yankees general manager Brian Cashman said he didn't know whether Jeter will be available to play on opening day. Jeter got an anti-inflammatory shot in his surgically repaired left ankle and missed his second straight exhibition.
Yankees third baseman Kevin Youkilis went 0 for 4 playing against his longtime former team.
Boston starter Felix Doubront allowed four runs and seven hits over 4 1/3 innings.
Yankees ace CC Sabathia pitched in a minor league game and gave up one run in six innings. He's set to start the opener April 1 against the Red Sox.