Major League Baseball is investigating after Alex Cora suggested that the Red Sox intentionally threw at New York Yankees star Aaron Judge over the weekend.

At issue are comments made by the Red Sox manager prior to Sunday’s series finale at Yankee Stadium. A day earlier, tempers flared when Yankees ace Gerrit Cole hit Rafael Devers with a pitch in the first inning of Saturday’s game. The Red Sox became convinced Cole hit Devers on purpose when he intentionally walked the Red Sox slugger his next time up in the fourth inning, and shortly afterwards the Red Sox appeared to retaliate when Brayan Bello threw a 97.4 mph sinker behind the 6-foot-7 Judge to lead off the sixth.

Cora effectively confirmed that was the case on Sunday morning after being asked if he expected the issue to linger into that afternoon’s game.

“(The matter) was closed yesterday, like around the sixth inning,” Cora told reporters. “We had our chance. It didn’t happen. We have to move on.”

A league source confirmed to the Herald that MLB is looking into those comments.

“It is being reviewed, which is a standard part of our process,” the source said.

If MLB determines any rules were broken, Cora, Bello or the Red Sox could potentially face league discipline. No decisions had been announced as of Monday afternoon.

Though Cora’s apparent admission that the Red Sox had thrown at Judge wasn’t subtle, he was crystal clear in his belief that Cole intentionally hit Devers because of the Yankees ace’s long-standing struggles against the All-Star third baseman.

Cora sounds off on Cole hitting Devers in 7-1 Red Sox win: ‘I’m not going to back off, it was intentional’

“It felt like the first at-bat, he hit on purpose,” Cora said postgame on Saturday. “He doesn’t want to face him, that’s the bottom line. He told us with the intentional walk that the first at-bat he hit him. He hit him, and we leave it at that. … We took exception to that because he was loud and clear that he didn’t want to face him.”

“They can say whatever they want, but the intentional walk was loud and clear: I don’t want to face him,” Cora added later. “It was intentional! I’m not gonna back off, it was intentional.”

Cole’s approach to Devers, both the hit by pitch and intentional walk, drew condemnation from Red Sox players as well. Devers said he felt Cole “panicked a little bit,” and Bello said he’d “shown a lot of weakness.”

Since the two first faced off in 2018, Devers has consistently gotten the better of Cole. The Red Sox third baseman is 15 for 42 (.357) lifetime with eight home runs, 21 RBI and eight walks against the Yankee right-hander over 51 plate appearances in the regular season and playoffs. Cole himself has acknowledged that few give him a harder time than Devers, and Saturday he told reporters the decision to intentionally walk him had been part of the team’s gameplan.

From the Yankees side, manager Aaron Boone denied any intention behind Cole hitting Devers.

“Definitely wasn’t throwing at him,” Boone told reporters postgame on Saturday. “Raffy was right on the line, and he threw a cutter trying to get it in there, and didn’t. I don’t think there was any intent from Gerrit there. … We’re not playing that kind of game.”

When informed of Cora’s comments about the Judge incident on Sunday morning, Boone expressed disappointment while noting the matter is now out of their hands.

“Yeah, that’s not allowed,” Boone said, per the New York Post. “That’s for somebody else to deal with. So we’re finished playing with them for now. So we’re on to Seattle now. But you can’t do that.”

Sunday’s series finale between the Red Sox and Yankees went off without any additional drama, with the Yankees clinching the series with a 5-2 victory. The loss dropped the Red Sox back to .500 at 75-75, and barring an incredible late-season turnaround that sees Boston surge back into the playoff picture, the two rivals won’t meet again until 2025.

Even though Judge didn’t wind up getting hit, he still got the last laugh on Sunday, belting a 445-foot home run to power the Yankees win. He told reporters afterwards he and Cora spoke, and while he declined to reveal the specifics, he said they had a good conversation.

“You play this game for a while, things like that happen,” Judge said. “I think they’re just protecting their players. Something’s gotta happen. That’s the way this game gets policed.

“I think the biggest thing is just don’t miss when you do it.”