NEW YORK (AP) - The New York Yankees filed an official protest with the commissioner's office after a disputed loss to the Florida Marlins.

New York manager Joe Girardi protested Sunday's 6-5 defeat at Florida because of a Marlins substitution mix-up in the eighth inning. Teams have 24 hours after a game to submit a protest, and Major League Baseball spokesman Pat Courtney confirmed Monday that the Yankees met the deadline.

Courtney said Bob DuPuy, baseball's chief operating officer, will rule on the protest. A decision is expected this week.

Generally, the commissioner's office tries to rule on protests within two days.

The Yankees were off Monday before opening a series in Atlanta on Tuesday night.

In an odd mix-up Sunday, Chris Coghlan started the top of the eighth in left field after Florida manager Fredi Gonzalez had removed him in a double switch. Alejandro De Aza batted for pitcher Renyel Pinto in the seventh and was supposed to take over in left, but never ran on the field.

Leo Nunez threw a pitch, then Girardi came out to protest. After about a 5-minute delay, Coghlan was removed, Jeremy Hermida went to left field and the Yankees played the rest of the game under protest. They were trailing 6-3 at the time.

Girardi thought Nunez should have been ruled out of the game once the mistake was recognized.

"But I'd like to keep the two runs I got in the ninth," the manager joked.