It came only five days after Hughes delivered his first homerless outing in a win against the Nationals. He had won each of his past three starts, but took the loss Wednesday, as his homer total reached 19 in 14 starts.
"He didn't really pitch any different," said manager Joe Girardi. "He just didn't locate as well."
David Ross' blast into the left-field seats marked the final blow against Hughes, following Jason Heyward's homer off the right-field foul pole an inning earlier and Martin Prado's solo shot just inside the left-field foul pole in the third.
Heyward crushed his fourth-inning blast high off the foul pole, then snuck his second homer into the right-field seats to tack on two more runs against Boone Logan in the eighth. But the Yankees made no excuses despite mid-90s heat, saying Atlanta's long balls would clear the shallow Stadium fences any day of the week.
"It's just that kind of ballpark," Heyward said. "But you've also got two teams capable of hitting a lot of home runs."
The Yankees proved it with their first swing of the day, as Derek Jeter sent Tommy Hanson's first-pitch fastball into the right-field seats. But Atlanta already had a 3-0 lead, and despite three more solo shots from Eric Chavez, Alex Rodriguez and Robinson Cano, the Braves would never relinquish their advanatage.
Michael Bourn led off the game with a single and stolen base, then scored on Dan Uggla's single to left field. After that, every Braves hit against Hughes was a home run.
Freddie Freeman started it, sending a first-pitch fastball into a Yankees bullpen that saw plenty of action after the shortest start by a New York starter in 20 games. Yankees starters had lasted at least six innings in their previous 19 starts before Hughes' exit.
"Ultimately, I think it's the first inning that's killing me more than anything -- coming out and not making good pitches," Hughes said. "It allows myself to get on a little bit of a roll, if I can have a solid first inning and go from there."
The bullpen kept it close for the next 2 1/3 frames -- when the Yankees hit three of their home runs -- but Heyward's second homer of the game in a three-run eighth inning rendered New York's four long balls meaningless.
Atlanta added another run in the ninth against Freddy Garcia with a pair of singles, rare for the matinee.
The Yankees could not find those hits when they needed to. A day after going 2-for-11 with runners in scoring position, New York went 1-for-4 in such situations to take its first series loss of June. Strong pitching and home runs had masked the lack of timely hitting during the recent 10-game winning streak, but not the past two games.
There were men on second and third in the second and eighth innings, but Jayson Nix popped out and Russell Martin grounded out to end those threats. There were runners on the corners in the seventh, but Rodriguez hit into an inning-ending double play.
"I feel way to good to have an at-bat like that," Rodriguez said. "It's not acceptable."
But like Hughes knows who he is, Girardi knows what his lineup is. It relies on the long ball, and with Hughes on the mound, it lost Wednesday's derby.
"I've said it all along," Girardi said, "we're going to score a lot of our runs on the home run. That's what we do."