Marcus Stroman threw one meatball from which his team couldn’t fully recover.

The righty served up a three-run home run to Jake Burger in the third inning, and the Yankees could only take a bite out of the deficit in a 5-2 loss to the Marlins in front of 36,295 in The Bronx on a chilly Wednesday night.

The Yankees had a chance to steal the game in the bottom of the ninth, when Jon Berti reached on an infield single and Anthony Volpe and Juan Soto walked, giving Aaron Judge a shot at another special moment.

But the Yankees captain flew out on a night his club went 0-for-7 with runners in scoring position, stranding 10 on base.

“We didn’t get the big hit,” manager Aaron Boone said after the Yankees failed to finish off a sweep and fell for just a third time in 13 games this season.

Stroman entered play with 12 innings pitched and zero earned runs allowed this year. His bid at a spotless season was disrupted with a 33-pitch third inning that nearly ended his night early.

Miami’s Nick Gordon worked a 10-pitch walk before Nick Fortes hit a slow bouncer to the right side, an area that Gleyber Torres had abandoned because Gordon had taken off to swipe second base.

The ball squirted through to the outfield, and Luis Arraez followed with an RBI single for the first earned run Stroman allowed in pinstripes.

But the second, third and fourth runs came two pitches later, when Burger smashed a middle-of-the-plate slider into the Marlins’ bullpen in left-center.

“Burger put a really good swing on a bad pitch,” said Stroman, who added he was “a little off” mechanically.

Stroman bounced back and completed five innings, allowing those four runs on four hits and four walks with seven strikeouts. His stuff was solid, but a movement and control specialist lost some of his command.

“I was just losing the zone,” said Stroman, whose team finished a 4-2 homestand and will begin a trip through Cleveland and Toronto on Friday. “It’s very uncharacteristic of me to walk four guys. That’s not me at all.”

Stroman had pitched well against the Astros in his club debut and went six scoreless innings in a loss to the Blue Jays on Friday. He has pitched about as well as the team could have hoped, but one bad inning dug a hole that the club didn’t escape.

Stroman rebounded, but his offense couldn’t.

The Yankees finished with just six hits and wasted several of the opportunities they did generate.

They put a pair of runners on in the fourth and fifth innings and failed to score. Judge grounded out in the fourth, and Alex Verdugo struck out before Berti grounded out in the fifth.

Giancarlo Stanton cracked his fourth home run of the season — and his first against his former team, meaning he has now homered against all 30 clubs — in the sixth inning for a first run. They added another in the eighth, when Juan Soto’s double drove in Volpe to make it 4-2.

But that was as close as they came.

A Volpe throwing error in the bottom of the eighth allowed Miami to score an insurance run that didn’t ultimately matter after Judge flew out.

“We just couldn’t quite finish it off,” said Boone, who earned his first ejection of the season in the seventh inning, when he disagreed with a low and outside pitch to Verdugo that home-plate umpire John Bacon called a strike.

For those looking for positives, Stroman lacked command and his best stuff yet still navigated his way through five innings.

After the troublesome third, Stroman faced the minimum in the fourth and fifth innings.

On a night that could have been worse, the Yankees did not have to empty their bullpen and got quality work from Luke Weaver, Victor Gonzalez and Dennis Santana.

Stroman was admittedly “off,” and the offense repeatedly failed in the clutch, but the Yankees were one swing away from escaping anyway.

Nine of their 13 games this season have been decided by three runs or fewer.