"They signaled to the bullpen before they announced to the umpire that he was hurt," Yankees manager Joe Girardi said.
Beckett left the game after allowing Robinson Cano's two-run double in the fifth inning, which gave the Yankees a 5-0 lead at the time.
Red Sox pitching coach John Farrell visited the mound, and after talking to Beckett, Farrell pointed first toward the Boston bullpen and then gestured to manager Terry Francona, who called in Manny Delcarmen to replace Beckett.
Because the umpires believed Beckett was being replaced due to injury, walking off with Red Sox assistant trainer Greg Barajas, Delcarmen was awarded as much time as needed to warm up.
Girardi said that the Red Sox had not properly noted that Beckett was hurt. Going by the letter of the law regarding Rule 8.03, Girardi contended that Delcarmen should have only been entitled to eight warmup pitches.
Delcarmen escaped the fifth inning, getting Francisco Cervelli to line out to left field for the final out. Between innings, Girardi protested the game to crew chief Larry Vanover.
"I think they're not going to hurt Manny Delcarmen," Girardi said. "That's the thing. But in my eyes, it was not done the right way. My thought is, Manny either gets eight warmup pitches and has to lob it, or they have to bring in a position player that is loose. One or the other. To me, he shouldn't get all of his pitches in."
New York has 24 hours to file a formal protest with the Commissioner's Office.
Red Sox manager Terry Francona was asked if he was surprised by the Yankees' decision to protest.
"That doesn't mean anything," Francona said. "John went out to talk to him. When Beckett said his back tightened up, Johnny looked at the umpire and said, 'We've got to get a pitcher,' and he said, 'OK.' After that, I didn't pay much attention."
The official rule regarding protests of MLB games is Rule 4.19, which reads:
"Each league shall adopt rules governing procedure for protesting a game, when a manager claims that an umpire's decision is in violation of these rules. No protest shall ever be permitted on judgment decisions by the umpire. In all protested games, the decision of the League President shall be final.
"Even if it is held that the protested decision violated the rules, no replay of the game will be ordered unless in the opinion of the League President the violation adversely affected the protesting team's chances of winning the game."
Girardi said that he did not know if there was a realistic chance the protest would be upheld and the game restored to the fifth inning.
"Obviously it could be used as a huge advantage if every time a guy was in trouble -- and I'm not saying that Beckett wasn't hurt -- but every time a guy was in trouble, you signal to the bullpen and it's, 'Oh, he's hurt,'" Girardi said.
The last Major League example of a game having a protest upheld and a game restarted was the June 16, 1986, game between the Cardinals and Pirates.
National League president Charles Feeney ruled with the Pirates' contention that the umpires had improperly called their 4-1 loss to the Cardinals with one out in the top of the sixth inning.
That game resumed on June 18, 1986, with St. Louis defeating Pittsburgh, 4-2, in a full nine innings.
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.