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.
"We're happy," Beltran said. "We won the series, it's important. This is the team that we're basically fighting. Hopefully when we face them again, we can expand our lead a little bit more."
Beltran, who had delivered big homers in the first two games of the series, was not so happy with his fielding in the finale. In the third inning, he helped sparked a Toronto burst after losing Troy Tulowitzki's flyball to right field in the sun.
"I lost it when it was getting close to me and I basically couldn't do anything," Beltran said. "Unfortunately, it would have been a different story if I had caught that ball."
Initially ruled an error, Tulowitzki was later credited with a two-out double. Josh Donaldson followed with an RBI single and Bautista piled on with his 28th home run for a 3-0 lead.
Manager Joe Girardi said blinding sun is "probably the toughest element a player has to deal with" and didn't fault Beltran for the miscue.
"It's unfortunate, it happens, but Carlos was pretty big for us this series," Girardi said.
New York hasn't swept a three-game set in Toronto since the opening series of the 2003 season, but the Yankees weren't beating themselves up after taking two of three to reclaim the division lead.
"I thought we did a good job coming in here and winning a tough series on the road," Girardi said.
On a whiteboard in the New York clubhouse, someone had written a message of encouragement that read "Cheer up everybody. We won the series. Still in first place."
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.
It came off rookie right-hander Luis Severino, who was making his third big league start.
"It was supposed to be a slider down," Severino said through a translator. "It stayed up and I paid for it."
Severino (0-2) struck out a career-best nine in six innings. He allowed three runs and five hits.
"It's pretty impressive to watch what he's done," Girardi said. "He has risen to the occasion."
The 21-year-old Severino is the youngest Yankees pitcher to fan nine in more than a century. Ray Keating was 20 when he did it against the St. Louis Browns on May 19, 1914.
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.
"He's been great at home and he was again today," manager John Gibbons said.
Toronto starting pitchers have gone 20 straight games without allowing more than three earned runs, extending the team record set Saturday.
"It's been a great stretch," Gibbons said. "Let's hope it holds up."
Jacoby Ellsbury had two of the three New York hits off Hutchison, including a two-out solo homer in the sixth.
Yankees third base coach Joe Espada was almost struck by Beltran's foul liner in the seventh.
Toronto optioned LHP Aaron Loup to Triple-A Buffalo after the game and will make a corresponding move before they play at Philadelphia on Tuesday.
REACHING NEW HEIGHTS
While in Toronto with his team, Yankees GM Brian Cashman did the CN Tower Edge Walk, a harnessed walk 1,168 feet above the city. Despite the harness, Cashman said the walk was scarier than his previous daredevil experiences, which include skydiving and rappelling down a building.
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.
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