KANSAS CITY, Mo. -- Joe Girardi second-guessed himself afterward for not protesting the game. If Dana DeMuth had any second-guesses about how he and his crew of umpires handled a disputed home run call in the bottom of the third inning, he wasn't saying.

A poor outing by Bartolo Colon and a miserable performance from the Yankees with runners on base led to a 5-4 loss to the Royals Wednesday night at Kauffman Stadium.

But afterward the talk was about a home run by the Royals' Billy Butler that perhaps shouldn't have been. The dispute revolved around the stadium ground rules.

"They're pretty explicit and clear," said Yankees first base coach Mick Kelleher, who went over the ground rules with the umpires before Monday's game.

"There was one question I had and it was about the top rail in left-centerfield. It was padded and the ball had to leave the ballpark and we talked about that twice . . . That ball didn't leave the ballpark so, to me, the way it was explained at home plate, that's not a home run."

Girardi, who said he will contact MLB today, asked several times for an explanation.

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"I was under the understanding that it had to go over both walls. Dana DeMuth said that it did not," Girardi said. "If he was incorrect, it would be a shame to lose the game that way."

Girardi said that in retrospect he should have protested the game. "I figured Dana knew the rules," he said. "Maybe I errored [in not protesting]. I believed the umpire."

DeMuth, through a Royals PR representative, declined to speak to a pool reporter, further incensing some Yankees.

An hour after the game, the umpires could be seen in their street clothes in the outfield near the wall. They were having a discussion that at times was animated with Steve Palermo, the former umpire who is an MLB umpire supervisor.

"That cost us the game," Mariano Rivera said. "I understand we're human, but you have replays and you get the call wrong? That's unacceptable."

Not everyone blamed the umpires. The Yankees left 11 on base and were 1-for-10 with runners in scoring position.

"I don't think the game was lost in that situation," Curtis Granderson said. "We had opportunities to come from behind."

The defeat cost the Yankees (74-47) a chance to take a 1½- game lead on the Red Sox, who lost to the Rays. The loss was most memorable because of the disputed home run by Butler in the critical four-run third.

The Yankees, trailing 5-3 in the ninth, scored once off Joakim Soria before Jorge Posada, on his 40th birthday, was called out on strikes with the bases loaded to end it. Soria staggered to his 22nd save after throwing 40 pitches, many not close to being strikes.

Derek Jeter, hitting .382 this month coming in, had four hits, and Granderson and Russell Martin homered. Granderson improved his team-best total to 34. Jeter was 9-for-15 in the series, raising his average to .290.

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Jeter singled off Soria with one out in the ninth, Granderson singled and Mark Teixeira walked to load the bases for the scorching Robinson Cano. He worked the count full on the seventh pitch of the at-bat before sending a sacrifice fly to left to bring in Jeter and make it 5-4.

A wild pitch moved the runners to second and third, and Nick Swisher walked to load the bases, bringing up Posada.

Colon came in 8-6 with a 3.31 ERA, unbeaten in his last four starts. He gave up five runs and seven hits in five innings.