TORONTO — A nasty splitter helped Nathan Eovaldi navigate and at times dominate one of baseball’s best lineups through four innings Thursday night. But the pitch flattened out on him at an inopportune time against the wrong hitter, leading to the Yankees’ 4-2 loss to the Blue Jays at Rogers Centre.

Reigning AL Most Valuable Player Josh Donaldson hammered a splitter for a three-run homer with two outs in the fifth, turning a 2-0 deficit into a 3-2 Toronto lead.

“It’s just frustrating,” Eovaldi said. “As well as I was throwing the ball tonight, I left that split up.”

Troy Tulowitzki’s homer, on a slider that came in with little movement, made it 4-2 in the sixth.

Said Joe Girardi: “Those two mistakes cost him.”

That was enough for Toronto ace and former Patchogue-Medford High School star Marcus Stroman. Other than a ragged, 34-pitch fourth inning in which the Yankees pushed across two runs, the 24-year-old right hander was terrific, allowing three hits in eight innings.

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Stroman (2-0, 4.22) had a 5.40 ERA after his first two starts of the season but entered the game with a 4-1 career record and 2.43 ERA against the Yankees. He struck out three, walked two and retired the final 11 batters he faced. The Yankees reached base in only two innings against him.

“It was what he does all the time,” said Alex Rodriguez, who went 0-for-3 and is hitting .120. “He keeps the ball down, he doesn’t give you too many fat pitches over the middle of the plate. A lot of hitters just pound the ball into the turf.”

Stroman followed his usual script, because of the 24 outs he recorded, 17 came on ground balls.

The Yankees (4-4), who will start a nine-game homestand Friday night against the Mariners, didn’t get a hit after the fourth inning.

“That was really the only good chance that we had to get some runs,” Girardi said. “He didn’t give us many opportunities. We didn’t square him up. Maybe squared up two or three balls, that was about it.”

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Roberto Osuna blew away the Yankees in a perfect ninth for his fourth save.

Eovaldi (0-1) was better Thursday night than he was April 7 against the Astros, when he got a no-decision in an 8-5 victory in which he gave up five runs and six hits in five innings. This time he allowed four runs, seven hits and two walks in 6 2⁄3 innings and had eight strikeouts.

After Eovaldi retired Chris Colabello to start the fifth, former Yankee Russell Martin worked a six-pitch walk. Eovaldi got Ryan Goins to fly out to center, but Kevin Pillar yanked a double off the third-base bag, putting runners at second and third for Donaldson.

He rifled a 1-and-0 splitter into the second level in dead center, an area visited by few baseballs in this building, for his fifth homer and a 3-2 lead.

“He was on top of his game,” Brett Gardner said of Stroman. “I thought Evo pitched great, too. Just Donaldson killed us with that big homer.”

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Tulowitzki jumped on a first-pitch slider an inning later for his second homer.

Defending American League East champion Toronto, which went 13-6 against the Yankees last season, won the series 2-1.

“We would have liked to get out of here winning two out of three,” A-Rod said. “We felt like we let one get away. But for us, it’s going to be nice getting home.”