Beckett had been skipped in his previous turn in the rotation because of back spasms.
The nasty conditions at Yankee Stadium -- raw, windy and wet -- probably didn't do Beckett's back any favors.
He hopes to make his next scheduled start on Sunday at Philadelphia, but it's too early to tell. Red Sox manager Terry Francona said that Beckett will be further examined by the team's medical staff on Wednesday in Boston.
"It was a pitch to [Alex] Rodriguez that he flew out to left on," said Beckett. "My footing just slipped, and it just got tighter and tighter after that."
The Red Sox wound up beating the Yankees, 7-6. Beckett took a no-decision.
The righty had just given up a two-run double to Robinson Cano before coming out of the game. Pitching coach John Farrell visited Beckett immediately after that double and motioned to the bullpen, apparently signaling that the righty had to come out of the game because of an injury. Manager Terry Francona and assistant trainer Greg Barajas came to the mound shortly thereafter, and Beckett walked off with them.
The Yankees, displeased with the sequence of events, announced in the sixth that they were playing the remainder of the game under protest because they weren't made aware of the fact that Beckett left the game with an injury.
"Protesting what? They didn't know I was injured? I don't really know [what to make of the protest]," Beckett said. "I just told [Farrell] kind of what I had and what happened. We just made the decision that it probably wasn't best for the rest of my body or the team to continue."
Beckett had mixed results in this one, giving up five hits and five runs over 4 2/3 innings. Two of the runs were unearned because of a fielding error by Red Sox shortstop Marco Scutaro in the second inning.
The season has been a struggle thus far for Beckett, who is 1-2 with a 7.29 ERA.
He originally tweaked his back at Fenway roughly 10 days ago while taking batting practice in preparation for Interleague Play.
"I don't think it's as severe as when I did it hitting," said Beckett. "You lose your footing, there's not a whole lot you can do."
Ian Browne is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.