The Blue Jays and the division-leading Yankees, separated by a half-game atop the AL East, will meet seven more times before the end of the season. Toronto swept a three-game series at Yankee Stadium last weekend.
New York's Carlos Beltran had delivered big homers in the first two games of the series. In the finale, however, he helped sparked a Toronto burst in the third inning after losing Troy Tulowitzki's flyball to right field in the sun.
Initially ruled an error, Tulowitzki was later credited with a two-out double. Josh Donaldson then hit an RBI single and Bautista piled on with his 28th home run for a 3-0 lead.
Bautista's drive was Toronto's first home run since Ryan Goins' three-run shot in the second inning of Thursday's 4-2 victory over Oakland. The Blue Jays have only had one three-game stretch this season in which they've failed to homer.
Hutchison (12-2) improved to 10-1 with a 2.57 ERA in 13 home starts, allowing one run and three hits in 6 2-3 innings.
Toronto starting pitchers have gone 20 straight games without allowing more than three earned runs, extending the team record set Saturday.
Making his third big league start, Yankees right-hander Luis Severino (0-2) struck out a career-best nine in six innings. He allowed three runs and five hits.
Jacoby Ellsbury had two of the three New York hits off Hutchison, including a two-out solo homer in the sixth.
Yankees: RHP Michael Pineda (forearm) was set to throw 45 pitches in a rehab start at Double-A Trenton.
Yankees: LHP CC Sabathia (4-9, 5.23 ERA) gets the start as New York returns home Monday to begin a three-game series against Minnesota. Sabathia is winless in five starts, although the Yankees have won three of those games. RHP Kyle Gibson (8-9, 3.75 ERA) starts for the Twins.
Blue Jays: After an off-day Monday, Toronto begins a two-game interleague series at Philadelphia on Tuesday. RHP R.A. Dickey (7-10, 3.96 ERA), who hasn't lost since July 9, seeks to win his fifth straight decision. RHP Aaron Nola (3-1, 4.25 ERA) will start for the Phillies.