A roster that Aaron Boone called “beat up” prior to Sunday’s game looked the part in a 5-1 loss to the Blue Jays, as the Yankees closed out a mediocre homestand by seeing Vladimir Guerrero Jr. knock them out again.

Guerrero’s sixth-inning homer and another lackluster showing from the offense spoiled what had been a strong start from Clarke Schmidt and sent the Yankees to their first series loss of the year.

“We’ve got to score more than we have here lately,’’ Boone said of his team that’s been held to three or fewer runs in all but one of its past seven games. “Part of it is we’re banged up. We’ve got to find ways. Right now, we’re struggling to roll out a crooked number.”

On Sunday, it was right-hander Kevin Gausman who shut down the Yankees over seven scoreless innings.

Their lone run came from Anthony Rizzo’s homer with two outs in the bottom of the ninth.

Schmidt retired the first 13 batters he faced and struck out a career-high eight before he faltered in the sixth.

He was hurt by Anthony Volpe’s first career error, as Volpe couldn’t come up with a George Springer grounder to shortstop with one out in the inning.

Bo Bichette followed with a hard grounder up the middle that a diving Gleyber Torres stopped and turned into a force out.

But Guerrero made the Yankees pay.

After starting the series by saying he would never play for the Yankees because of “personal” reasons and then taking issue with being hit by a pitch on Friday, Guerrero put another imprint on the series when he followed Bichette’s force out with a rocket home run to left to give Toronto a 2-0 lead and then took his time and put on a bit of a show as he circled the bases.

“It was a big home run and if he wants to celebrate, that’s fine,’’ Kyle Higashioka said. “For me, the best remedy is to get him out every time and we didn’t do it today.”

Boone said he had Michael King ready in the bullpen, but wanted to get Schmidt through the inning.

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“Obviously, it cost us,’’ Boone said.

Volpe took the blame for the inning due to the miscue he made on the Springer grounder.

“That was a mistake breaking ball over the heart of the plate,’’ Schmidt said of the pitch hit out by Guerrero. “He does a really good job with mistakes and hitting breaking balls.”

Schmidt then faced lefty-swinging Daulton Varsho, who hit one into the second deck in right field to make it 3-0 and end Schmidt’s day after three unearned runs.

“It leaves a sour taste in your mouth,’’ Schmidt said. “Overall, I’m happy with the progress I made and I’ll take this one and get on a little roll here.”

Schmidt entered with a 8.79 ERA after four miserable starts in which he hadn’t lasted more than four innings, but he was perfect through the first 4 ¹/₃ innings on Sunday before Matt Chapman doubled down the first-base line with one out in the top of the fifth.

The Yankee lineup was no match for Gausman, who struck out 11.

“We’ve got to keep pushing now when it’s tough and we’re grinding offensively,’’ Boone said.

The only drama came after Rizzo’s homer in the ninth, when Gleyber Torres and DJ LeMahieu followed with singles before Oswaldo Cabrera popped out to end it.

LeMahieu lined a double to center to start the bottom of the fifth, misplayed by Kevin Kiermaier, but the light-hitting bottom half of the lineup couldn’t get anything going, as Cabrera, Oswald Peraza and Higashioka all struck out.

King gave up back-to-back doubles to Whit Merrifield and Danny Jansen in the seventh, as the Blue Jays extended their lead to 4-0.