Nestor Cortes (4-2) allowed two runs and five hits in six-plus innings to snap a four-start winless streak. He struck out six and walked one.
“Just a great way to finish off what was a very good series for us,” Yankees manager Aaron Boone said.
Anthony Volpe also homered for the Yankees, who took three of four from Toronto. The rookie shortstop made it 4-2 with a solo shot off Nate Pearson in the ninth, his seventh of the season.
The Yankees have hit 33 home runs in 17 games this month.
“I feel like we’re rolling now,” Cortes said. “I feel like we’re playing really good baseball. The dugout is coming alive.”
Ryan Weber worked one inning, Albert Abreu pitched the eighth and Ron Marinaccio finished for his first career save.
“We called that Nestor and the Funky Bunch tonight,” Boone joked, acknowledging that the quartet of Michael King, Clay Holmes, Jimmy Cordero and Wandy Peralta were all unavailable.
“It’s one of those days where a lot of your big boys are down and you’ve just got to find a way,” Boone added.
Bo Bichette homered in the bottom of the first, but Toronto lost its first home series of the season after winning five straight.
José Berríos (3-4) allowed three runs and six hits in 6 2/3 innings, losing for the first time since April 19 at Houston. He walked one and struck out eight.
Judge connected on a 1-1 pitch from Berríos after Gleyber Torres led off the game with a single.
“That was big, and then Nestor kind of took it from there,” Boone said. “AJ setting the tone right out of the gate was nice.”
The homer was Judge’s 12th of the season and sixth in six games. The reigning AL MVP homered four times in the series, including going deep twice in Monday’s opener and hitting a tiebreaking shot in the eighth inning of Tuesday’s 6-3 win.
Judge said his powerful series wasn’t motivated by resentment after he was accused of sign stealing Monday when the Toronto broadcast caught him peeking away from home plate before homering off Blue Jays reliever Jay Jackson. Jackson later acknowledged he was tipping his pitches.
“I’m just trying to do my job,” Judge said. “I was upset, but nothing I can do about that. I’ve still got to go out there and play.”
Judge has six home runs among his last nine hits. He almost connected for a second time in the sixth, but replay review showed his deep drive hit the top of the wall in center, overturning the call on the field. Judge ended up with a double.
“These last four days, he’s been locked in,” Berríos said.
New York chased Berríos and made it 3-1 in the seventh when Oswaldo Cabrera doubled and scored on a two-out single by Aaron Hicks, who went 3 for 4.
Held out of the starting lineup because of a sore right knee, Blue Jays slugger Vladimir Guerrero Jr. came off the bench to pinch hit for Santiago Espinal with the bases loaded in the bottom of the seventh. Guerrero hit a sacrifice fly on the first pitch he saw from Weber to make it 3-2.
Yankees: RHP Tommy Kahnle (right biceps tendonitis) struck out one in a scoreless inning for Class-A Tampa on Thursday, his first rehab appearance. Boone said Kahnle will make at least four rehab appearances. ... New York put C Jose Trevino (strained left hamstring) on the 10-day injured list and recalled C Ben Rortvedt from Triple-A. ... Boone said RHP Ian Hamilton (strained right groin) is expected to miss four weeks. Hamilton was placed on the 15-day injured list Wednesday.
New York 3B Josh Donaldson’s return from a strained right hamstring has been delayed after the infielder sliced his thumb, Boone said.
“He was putting something together at home with his daughter and cut his thumb, so it kept him from hitting for a couple of days,” Boone said, adding that Donaldson is close to beginning a minor league rehab assignment.
Judge has 32 career home runs against the Blue Jays, more than any other Yankees player. Jorge Posada homered 31 times against Toronto. Judge has gone deep 16 times in 41 career games in Toronto.
SEE YOU IN SEPTEMBER
The Blue Jays and Yankees don’t meet again for four months, squaring off next in a three-game series in The Bronx that starts September 19.
“When you continually play a team over and over and over again, it starts to get a little bit annoying,” Hicks said. “Now that we don’t see them for a while, it’s nice. You can play other teams.”
Yankees: RHP Clarke Schmidt (1-4, 6.30) starts Friday as the Yankees begin a three-game series in Cincinnati. RHP Ben Lively (1-1, 1.69) starts for the Reds.
Blue Jays: LHP Yusei Kikuchi (5-0, 3.89) starts Friday as Toronto begins a three-game series against Baltimore. RHP Kyle Gibson (4-3, 4.67) goes for the Orioles.
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