Kyle Drabek limited the Yankees to three hits over seven innings to hand New York its third loss in four outings. The Blue Jays ended a three-game skid.
Arencibia hit a two-run homer in the second and Encarnacion produced a three-run blast in the third. It was Encarnacion's 13th home run of the season. Jose Bautista added a solo shot for the Blue Jays in the fifth and Kelly Johnson had another in the seventh.
Drabek (3-4) gave up a lone run while striking out five and walking four.
Hiroki Kuroda (3-5) allowed seven runs on eight hits while throwing 101 pitches in five innings to take the loss.