Kevin Correia, who was also Pittsburgh's Opening Day pitcher last season, pitched two hitless innings in his first outing.
"The first game is always a little weird, especially pitching from the stretch," said Correia, who issued consecutive two-out walks in the first.
"But my arm feels fine. Everything feels as good as it did at this point last season," added Correia, who got off to a terrific start in 2011, his first season with the Pirates, wining five of his first seven decisions.
After the Pirates (2-2) made it 3-1 with an unearned run in the fourth, Francisco Cervelli's sacrifice fly in the sixth pulled the Yankees (2-2) within one run at 3-2.
Nate McLouth put the Bucs back up by two when his run-scoring single in the seventh made it 4-2.
Hughes, battling for a spot in the Yankees' rotation following a troublesome 2011 season, had a rocky spring debut in which he was not able to complete his targeted two innings. In 1 1/3 innings, he was charged with four hits and two runs, one of them earned.
"You don't want to see runs score and things like that, but from a physical standpoint, it felt pretty good for the first time out," Hughes said. "I was having a little trouble keeping the ball down. I was probably a little anxious and maybe overthrowing a little bit, but overall, it was decent."
Ryota Igarashi and Juan Cruz, two non-roster right-handers competing for a spot in the Pirates' bullpen, each made his second scoreless one-inning outing of the spring.
Up next: A mere technicality with all pitchers pulling short stints, but the Pirates face a right-handed starter for the first time, Toronto's Kyle Drabek, in Wednesday's 1:05 p.m. ET game at McKechnie Field. Jeff Karstens will make his second start, and he is expected to stretch out to three innings. Pedro Alvarez, hitless in five at-bats with three strikeouts, will be back at third base after sitting out Tuesday's game.