Bautista's one-out blast off David Robertson (2-4), his major league-leading 40th round-tripper of the year, broke a 2-2 tie.
Bautista had smacked his 39th homer in the third inning -- a two-run shot that erased a 1-0 Yankees lead and gave Toronto a lead that stood until Jorge Posada's RBI double in the sixth.
Scott Downs (5-5) was credited with the win after pitching a scoreless eighth and Kevin Gregg secured his 28th save. Blue Jays starter Brandon Morrow fanned 12 Yankees in six innings.
New York's Ivan Nova, in his first major league start, allowed two runs in 5 1/3 innings.
The Yankees' American League East lead over second-place Tampa Bay dwindled to one-half game. The Rays were visiting the Los Angeles Angels Monday.