NEW YORK — Perched near the top step of the Yankees dugout, Aaron Boone shook his head as Gleyber Torres appeared to plead his case, having been replaced at second base for the top of the fourth inning. The manager focused on the blue lineup card in his hands, scribbling ink across the folded sheet of cardboard.

Having jogged on a long single before being tagged out at home plate on a double, Torres watched the final six innings from the clubhouse and dugout for disciplinary reasons as the Yankees fell to the Blue Jays, 8-5, on Friday evening at Yankee Stadium.

“I feel really sorry for whatever I [did] tonight, especially for the fans and also for my teammates,” Torres said. “I’m a human being. I made an error. I feel like whatever I [did] tonight, I’m going to learn a lot. I just want to compete with my teammates. I want to play great.”

Boone’s decision to substitute Oswaldo Cabrera for Torres followed Torres’ slow trot on a 363-foot drive on a pitch from Toronto’s Kevin Gausman in the second inning. The ball struck the left-field wall as a surprised Torres reached first base.

“I thought it was a homer; unfortunately, it’s just a single,” he said.

One batter later, the inning ended as Torres was sent home by third-base coach Luis Rojas on an Anthony Volpe double, tagged out at home plate by Blue Jays catcher Brian Serven. It was at that point, Boone said, that he decided he would remove Torres from the game.

“I just felt like I needed to in that spot,” Boone said. “I’m not going to get too far down the rabbit hole of making judgments on this one. I just felt like, in that moment, I needed to do that. Simple as that. It is what it is, it’s over with, and we’ve got to move on. He and I have spoken, and hopefully this is a great learning moment for all of us.”

Oddly, Torres returned to the field to play defense in the third inning before Boone substituted for him in the fourth. Boone indicated that he allowed Torres to do so because he had made the final out of the inning, and Boone “didn’t want to ambush Cabrera with the quick turnaround” to get on the field.

In June, Torres was benched for performance-related reasons, as well as failing to run out a ground ball against the Mets at Citi Field. At the time, Boone noted that a groin injury had slowed Torres. Torres said on Friday that no physical issue kept him from running hard.

The developing situation with Torres — a potential free agent who indicated that he had little interest in adding third base to his portfolio following the Yanks’ acquisition of Jazz Chisholm Jr. — provided a meaty subplot to a contest in which Aaron Judge hit his Major League-leading 40 th home run and Volpe also hit his 10th homer.

The Yankees never led, falling behind early as Marcus Stroman was thumped for seven runs and eight hits in 2 2/3 innings. The veteran right-hander had a 2.60 ERA through May but has struggled since, pitching to a 6.32 ERA (33 ER / 47 IP) across his last 10 starts.

Stroman’s average fastball velocity dipped to 88.8 mph, and Boone said that he made mistakes with secondary pitches over the heart of the plate.

“The offense did enough to win the game,” Stroman said. “The loss is definitely solely on me. I just didn’t execute; just out of rhythm mechanically and had no feel for my pitches. Just a frustrating one.”

Judge said that he had spoken to Torres in his role as team captain, but declined to provide specifics. Judge said he thought it “speaks volumes” that Torres returned to the bench after cooling off in the clubhouse, adding, “He could have run and hid.” Judge also said he believed the benching would serve as a message to the rest of the team.

“If I know Gleyber, something like this ain’t going to happen again,” Judge said. “He takes pride in his work and his craft. He’s definitely not happy about what happened. I bet you the rest of his career, something like this ain’t going to happen again.”