The Blue Jays downed New York for the second straight night and the Yankees have lost four out of five.
New York's only run came on a home run by Robinson Cano in the first, but the Yankees managed only five hits overall against Drew Hutchison (3-1) in his six-inning stint.
Bautista put Toronto in front with his two-run blast in the third and Arencibia's homer came in the seventh.
Phil Hughes (3-5) gave up the first two runs along with seven hits in 5 1/3 innings to take the loss.
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