The Yankees were down 5-1 after five innings but turned it on down the stretch, scoring eight runs in the final four frames to retain a share of first place in the American League East with the Baltimore Orioles.
With the victory, New York earned a split in its four-game set with the Blue Jays and now will visit the Tampa Bay Rays for the final three games of the regular season.
Boone Logan (7-2) recorded two outs to record the victory.
Darren Oliver (3-4) was tagged with the loss for Toronto.
Brett Lawrie went 3-for-5 with a two-run homer for the Jays.