Martin Prado, who opened the bottom of the third with a homer, then lined a pitch to left field that Yoenis Cespedes could not grab before it bounced off the wall. Prado was running toward second base out of the batter's box, but Beltran and McCann held up at second and first, respectively, to make sure the ball was not caught.
When the relay throw came in from the outfield, Prado was too close to second base, which was occupied by McCann. Prado was eventually tagged out in a brief rundown for the first out of the inning, and New York did not score on the play.
"It's tough, because we gave them one out," manager Joe Girardi said. "It looked like we were getting to [Kelly] and that was a big out for him."
Red Sox manager John Farrell was glad to get the key out.
"Rather than potentially a run in and no outs on the board, we catch a break with an out," said Farrell. "And the way that inning was unfolding, it had a chance to be a bigger inning for them."
The Yankees did push across two runs in the inning. Kelly walked the next two batters and Derek Jeter drove in a run on an infield single later in the inning, but the Yankees still trailed, 7-3.
The worse news came later in the game when Prado felt something in his left hamstring that caused him to be removed in the ninth inning for a pinch-hitter, Chris Young.
Prado was evaluated by Yankees team physician Dr. Christopher Ahmad after the game and was diagnosed with a tight left hamstring with further tests to come on Wednesday.
Prado had been one of the few Yankees bright spots at the plate lately. In his last 16 games overall, he is hitting .381 with 12 runs, six doubles, four home runs and 11 RBIs. He has homered five times in 29 games with New York after hitting just five in 106 games with Arizona.
"That's not someone that we want to lose," Girardi said. "He's played extremely well. We'll just have to see how he is."