A spokesman for Major League Baseball confirmed to The Associated Press on Wednesday night that the commissioner's office received the official paperwork before the early Thursday deadline.
New York claimed there was no indication of an injury to Red Sox starter Josh Beckett before he came out in the fifth inning. Still, reliever Manny Delcarmen was given all the time he needed to warm up on a damp and chilly night.
The Yankees, who were leading 5-0 at the time, protested to umpire crew chief Larry Vanover after the inning. The team then had 24 hours from the final out of Tuesday night's 7-6 loss to submit its protest to the commissioner's office. The game ended early Wednesday, about 13 minutes after midnight.
MLB is expected to respond within five business days. Bob DuPuy, baseball's chief operating officer, normally rules on protests.
Boston put Beckett on the 15-day disabled list Wednesday with a lower back strain. The right-hander had skipped his previous turn in the rotation because of back spasms.
General manager Brian Cashman explained, however, that the issue for the Yankees was not whether Beckett was hurt. Their protest centers on the way he was removed from the game and whether Delcarmen should have been given only the standard eight pitches to warm up.
When a pitcher leaves a game with an injury, baseball rules allow for his replacement to take as much time as needed to get loose.
Following Robinson Cano's two-run double in the fifth, Boston pitching coach John Farrell visited the mound. After a quick consultation with Beckett he gestured to the bullpen, and plate umpire Angel Campos signaled Delcarmen into the game.
Then, a trainer and Red Sox manager Terry Francona went to the mound as Delcarmen got ready to enter.
"To me, he shouldn't get all his pitches there," Yankees manager Joe Girardi said after the game. "In my eyes it was not done in the right way. Anytime a guy is in trouble, you signal to the bullpen and say, 'Oh, he's hurt.' That's a huge advantage."