Estrada (5-7) allowed five hits and three walks while striking out six in going seven innings for the third straight start. He had gone 12 starts without a win.
In taking the rubber match of the three-game series, the Blue Jays (54-60) have a 7-6 lead in the season series with the Yankees (60-53).
Sonny Gray (6-7), starting for the second time since the Yankees obtained him in a trade with the Oakland Athletics, allowed four hits, four walks and three runs (two earned) in six innings. The right-hander struck out six and is 0-2 with the Yankees.
Ezequiel Carrera doubled with one out in the second inning, took second on Gray's errant pickoff attempt and slid home safely after the pitcher scooped the ball to catcher Gary Sanchez on a trickler by Ryan Goins.
The Blue Jays went up 2-0 in the third on a walk and stolen base by Jose Bautista, and a single by Josh Donaldson.
Toronto took a 3-0 lead in the fourth. Pearce led off with a single, Carrera sacrificed him to second, Goins walked and Kevin Pillar rapped an RBI single to left.
Bautista hit his 19th homer of the season with two out in the seventh against reliever Chasen Shreve to increase Toronto's lead to four runs.
Toronto's Ryan Tepera pitched around a single in the eighth and Roberto Osuna pitched around two walks by striking out three in the ninth.
NOTES: Yankees OF Clint Frazier (left oblique strain) went on the 10-day disabled list Thursday and OF Aaron Hicks (right oblique strain) was reinstated from the DL. ... Toronto RHP Taylor Cole (fractured right toe) was put on the disabled list Thursday after he was hit on the foot by a comebacker during his major league debut Wednesday. RHP Chris Smith was recalled from Triple-A Buffalo to take his place. ... Toronto DH (illness) was a late scratch Thursday and RF Jose Bautista moved to DH and OF Ezequiel Carrera played right field. ... Yankees LHP Jaime Garcia (5-8, 4.49 ERA) will face Boston Red Sox LHP Eduardo Rodriguez (4-3, 4.08) Friday in New York. ... RHP Marcus Stroman (10-5, 3.17) will oppose Pittsburgh Pirates RHP Jameson Taillon (6-5, 4.60) Friday in Toronto.