Beltran had three hits and was pressed into his first career appearance at first base for the banged-up Yankees. Ichiro Suzuki robbed David Ortiz of extra bases with a spectacular catch in the eighth inning.
Mike Napoli homered and Felix Doubront (1-2) went 6.2 innings.
New York, playing without Derek Jeter for the second consecutive game, scored its third run with the benefit of instant replay in the fourth.
With runners at the corners and one out, the Red Sox thought they turned an inning-ending double play on Francisco Cervelli’s grounder. First base umpire Bob Davidson called Cervelli out on a bang-bang play, and Cervelli grabbed his right hamstring as he tumbled to the ground.
Yankees manager Joe Girardi challenged the call, which was overturned after a 3-minute replay review. That gave New York another run and a 3-1 lead.
Farrell, surely still bothered by a replay review that curiously went against Boston the day before, pointed to his eyes as he argued with two umpires. He was quickly ejected by Davidson.
Managers aren’t allowed to argue replay rulings.
Major League Baseball acknowledged it made the wrong call on a replay challenge that went against the Red Sox during New York’s 7-4 victory Saturday.
Cervelli was replaced at first base by Suzuki. When the Yankees took the field in the fifth, Suzuki was in right field and Beltran moved from right field to first base to replace Cervelli.
It was the first time Beltran had played first base in his 16-year major league career. He was pressed into service because oft-injured second baseman Brian Roberts was sidelined with a sore back, preventing Girardi from shuffling his infielders after Cervelli went down.
David Phelps struck out pinch-hitter Mike Carp with the bases loaded to end the eighth, pumping his fist as he bounced off the mound. Shawn Kelley struck out two in a perfect ninth for his third save.
Jacoby Ellsbury made a sliding catch in left-center to end it.