Hughes (13-11) surrendered four hits, worked around three walks and struck out five in the victory, his third straight in which he has yielded two earned runs or fewer.
Nick Swisher provided a run-scoring single in the third inning and Curtis Granderson added a fourth-inning sacrifice fly to account for the Yankees' offense.
Toronto's Ricky Romero (8-12) dropped his 11th straight decision despite allowing only two runs on five hits through seven full frames.
Adeiny Hechavarria socked a solo homer in the fifth to supply the Blue Jays' only run.
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