Jeter tied a career high with the performance and Nick Swisher contributed a two-run shot for the Yankees, won won for the seventh time in eight games.
New York also got a solo blast from Alex Rodriguez in the victory.
CC Sabathia (19-7) picked up his third straight winning decision, surrendering six hits and two runs over 7 2/3 innings while fanning 10 with one walk.
Toronto's Brett Cecil (4-8) absorbed the loss in a six-inning effort, giving up five runs (four earned) on five hits.
Jose Bautista belted his 40th homer of the year -- a solo shot -- as the Blue Jays dropped their eighth decision in 11 games.