New York remained tied with Baltimore atop the American League East after the Orioles defeated Tampa Bay in 14 innings earlier in the day.
Baltimore and New York will not meet again in the regular season. The Yankees will play their next nine games at home against Tampa Bay, Toronto and Oakland.
Hughes (15-12) allowed five hits and walked only one. He gave up a leadoff double in the eighth to Pedro Ciriaco and, after retiring pinch-hitter Mauro Gomez on a fly ball to center, was removed in favor of Boone Logan.
Rafael Soriano worked the ninth for his 38th save.
Felix Doubront (10-9) took the loss, surrendering both runs on four hits with five walks in 6 1/3.