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06/23/09 6:16 PM ET

Yankees' protest denied by MLB

Sunday's result will stand up as a victory for Marlins

ATLANTA -- The Yankees' 6-5 loss to the Marlins on Sunday will remain just that -- a loss.

Major League Baseball on Tuesday afternoon denied a protest filed officially by the Yankees on Monday, allowing the final result at Land Shark Stadium to hold up and completing a series where New York lost two out of three games to Florida.

Two days removed from the on-field protest, which caused a lengthy delay in the eighth inning of play, Yankees manager Joe Girardi reserved further comment until he could hear more about the ruling. Girardi was first informed of MLB president and chief operating officer Bob DuPuy's decision by reporters at Turner Field.

"I still think it's kind of funny what happened, interesting," Girardi said. "I've thought about it many times."

Girardi said he spent time on the phone during the Yankees' off-day on Monday going over the content of the filing with general manager Brian Cashman and assistant general manager Jean Afterman.

The protest dates to the top of the eighth inning on Sunday, when Marlins manager Fredi Gonzalez made an improper substitution.

In the bottom of the seventh inning, the Marlins pinch-hit outfielder Alejandro De Aza for pitcher Renyel Pinto, who was batting ninth. When the inning ended, Gonzalez informed home-plate umpire Tim Timmons of the changes. De Aza was to remain in the game and play left field in place of Chris Coghlan. Reliever Leo Nunez entered the game, and he was positioned in Coghlan's leadoff spot.

However, when the eighth inning started, Coghlan was in left field. Nunez threw one pitch to Derek Jeter, a called strike. At that point, Girardi brought to the attention of the umpires that Coghlan was supposed to be out of the game, with De Aza in left field.

Girardi compared the snafu to a May 17 mix-up by Rays manager Joe Maddon, who listed both Evan Longoria and Ben Zobrist as the club's third baseman, though Longoria was supposed to be the designated hitter. The Rays lost the DH for that game, though Longoria was incorrectly permitted to reenter the game by the umpires.

"To me, it seems kind of similar to the situation with the third basemen, where the guy who played the field was the guy who stayed," Girardi said. "Coghlan was the first guy in the first slot in the batting order. And then they put the pitcher in. So I think the first guy should stay."

For more than five minutes, play was delayed, eventually with Coghlan leaving the field. De Aza headed to left field, only to be replaced by Jeremy Hermida. The Marlins were leading, 6-3, at the time.

Umpire crew chief Jeff Kellogg outlined the protest after the game: "We're going to file an incident report and all that. The protest is over, the pitcher should have been removed from the game, or the pitch should not have counted. That's the protest. Either or. One or the other should have happened."

The Yankees were hoping the game would be resumed in the top of the eighth inning, with Jeter at the plate and the score at 6-3. In Miami, Gonzalez said the protest made for a restless off-day on Monday.

"For me, it wasn't something you could protest," Gonzalez said. "It's embarrassing. Big-time embarrassing. You feel like you've got 25 guys, six coaches, staff members, [35,000] people in the stands and two million viewers [watching]. I'll tell you what, it's not easy. It's embarrassing. To get the protest and an off-day, it's a tough couple of days."

Working in favor of the Marlins was Rule 3.05, which states:

"If an improper substitution is made for the pitcher, the umpire shall direct the proper pitcher to return to the game until the provisions of this rule are fulfilled. If the improper pitcher is permitted to pitch, any play that results is legal. The improper pitcher becomes the proper pitcher as soon as he makes his first pitch to the batter, or as soon as any runner is put out."

Additionally, the Rule 3.05 (c) comment reads: "If a manager attempts to remove a pitcher in violation of Rule 3.05 (c) the umpire shall notify the manager of the offending club that it cannot be done. If, by chance, the umpire-in-chief has, through oversight, announced the incoming improper pitcher, he should still correct the situation before the improper pitcher pitches. Once the improper pitcher delivers a pitch, he becomes the proper pitcher."

Bryan Hoch is a reporter for MLB.com. Joe Frisaro, a reporter for MLB.com, contributed to this story. This story was not subject to the approval of Major League Baseball or its clubs.