The Washington Nationals’ disappointing season reached a dreadful new low Sunday afternoon. The day after the Nationals were eliminated from playoff contention, lightning-rod closer Jonathan Papelbon had his left hand around star outfielder Bryce Harper’s throat in a quarrel that was broken up by teammates in the bottom of the eighth inning of a woeful 12-5 loss to the Philadelphia Phillies.

After Harper flied out and jogged to first base, he walked toward the dugout, where Papelbon, standing at the railing, said, “Run that out” and more. Papelbon followed Harper to the dugout steps and kept talking, eventually shouting. Harper stopped, looked at Papelbon and yelled back, saying at one point, “Let’s . . . go.”

Then Papelbon reached for the neck of the face of the franchise, pushing Harper back against the wooden dugout bench. Harper reached for Papelbon’s chest, grabbing fistfuls of jersey. The teammates wrestled against the bench, and Ian Desmond jumped in to pull Harper away to the other end of the dugout. Pitching coach Steve McCatty and hitting coach Rick Schu held Papelbon back.

“I’m in the wrong there,” Papelbon admitted later.

Harper stormed off to the tunnel leading to the clubhouse and didn’t take the field in the ninth as Tyler Moore entered the game and Matt den Dekker moved from left field to right. Papelbon, who got the last out of the eighth inning, stayed in with the score tied and gave up a two-home run to Andres Blanco. Papelbon drew loud boos from fans at Nationals Park and was finally pulled after 32 pitches. He was charged with five of the eight runs the Phillies scored in the ninth.

“This is a family issue, and we’ll deal with it that way,” said Manager Matt Williams, who was at the other end of the dugout during the fight. “There was an altercation in the dugout, and we’ll leave it at that.”

Immediately after the game, Williams told reporters that he left Papelbon in the game because “he’s our closer.”

Late Sunday, in the face of mounting criticism for his move, Williams took the unusual step of calling reporters to offer a revised explanation.

The reason he sent Papelbon back in, Williams said, was that he didn’t know the details of the fight that took place just a few feet from him in the dugout.

“Now that I’ve had a chance to view the videotape, I would absolutely not have sent him back out there,” Williams said Sunday night. “I didn’t have the luxury of viewing that at that time, with one out in the eighth inning. And I’m livid about it.”

After the game, Papelbon apologized to Harper, but the two players took different tones.

“He apologized, so whatever,” Harper said during his brief postgame comments. “I really don’t care. It’s like brothers fighting.”

Papelbon also stuck to the family theme, referring to the fight as one among brothers that can be quickly forgotten. But asked whether he had ever fought a teammate, Harper had a telling response: “[I’m] usually fighting the other team.”

Williams said the Nationals hadn’t yet discussed any discipline for Papelbon, who said he didn’t expect any. “We’ll handle that all in-house,” Papelbon said. General Manager Mike Rizzo didn’t respond to a request for comment after the game.

Papelbon tried to take a positive tone about the postgame talk with Harper. He said things aren’t always “hunky dory” during the long baseball season and that disagreements happen when emotions spill over.

“I didn’t maybe necessarily do it the right way, and there’s better ways to do it,” Papelbon said. “But it happened. I can’t take anything back. Bryce and I are good, and we will be good. We have a brotherly relationship, everyone in this clubhouse. We’ll be good, and we’ll get better from this. I truly do think that we’ll get better from this. Our relationship will get better from this. Next year when we are in the thick of it and we are grinding together and big games mean something, we’ll pick each other up.”

Plenty of misery has surrounded the Nationals this season, but the team’s closer attacking the best player on the team and a top NL MVP candidate is a new low. The fight overshadowed a nice moment for Desmond in likely his second-to-last home game as a National. The soon-to-be free agent was replaced defensively before the ninth inning and left the game to a standing ovation.

“That stuff just happens,” Desmond, who is close with Harper, said of the fight. “It’s been an emotional couple days, and when emotions boil over sometimes, it gets the best of us and no blood drawn. I think we’ll be all right.”

Desmond smacked three hits, including a home run, on Sunday. He and den Dekker, who also had three hits, powered the offense. Catcher Jose Lobaton, another who helped break up the fight in the dugout, had a key double in the seventh, when the Nationals took a 4-2 lead.

But reliever Casey Janssen lost the lead in the eighth on a two-run home run by Jeff Francoeur. Janssen was replaced by Felipe Rivero, who gave up a hit to the only hitter he faced and was pulled in turn for Papelbon.

Then came the series of events that sunk the Nationals to new depths, leaving many, including the fans at Nationals Park for Fan Appreciation Day, with an image that will be difficult to forget.