NEW YORK — Roger Federer was a twitchy, unsettled mess, channeling his inner Serena Williams by lecturing the chair umpire. And this was after he had won the third set.

The crackling forehands of his 20- year-old opponent, Juan Martin del Potro bothered him. Del Potro’s sneaking glances toward his coach before he would ask for a call to be challenged bothered him. The swirling winds, the blowing trash, the noisy crowd — these were moments of imperfection unappreciated by the tennis maestro.

All these bothers added up until there was del Potro of Argentina standing in the middle of the court, holding up a trophy, winner, 3-6, 7-6 (5), 4-6, 7-6 (4), 6-2, over the five-time defending champion in the finals of the U. S. Open Monday night at Arthur Ashe Stadium.

After a Federer backhand flew long, on his third championship point, del Potro dropped to the ground, flat on his back. Looking at the sky, it must have been how Federer had felt all match, trying to solve the game of the 6-foot-6 del Potro, now the tallest Grand Slam tournament winner.

“I don’t have words to explain it,” del Potro said of his victory.

This was the first Open final to go the ultimate five sets since 1999. Del Potro is the first Argentine man since Guillermo Vilas in 1977 to win the U. S. title, and Vilas was in the stands Monday standing and cheering for del Potro.

Federer had won 40 consecutive matches here in ways both dominating and imperious but almost never did he become unsettled the way he did this time.

During the four-hour, six-minute match, Federer was overheard on national television muttering an audible obscenity and engaging chair umpire Jake Garner in a tempestuous argument over how del Potro was using the challenge system.

“Don’t tell me to be quiet, OK?” Federer said to Garner. “When I want to talk, I talk.”

At the post-match news conference, Federer reminded reporters where he stood on challenges in the first place.

“You know what I think about Hawk- Eye,” he said. “Shouldn’t be there in the first place. So then the second question shouldn’t happen. It is what it is.”

By the fifth set, del Potro was knocking the 28-year-old Federer to his knees with his monstrous forehand. Federer, the father of baby twin daughters, was made to look clunky when he was forced to block back a del Potro serve or when he could only turn his head to watch a passing shot from del Potro skim past his face.

Federer had last lost in this tournament against another Argentine, David Nalbandian. He had been the heavy favorite to become the first man since Bill Tilden in 1925 to win six consecutive Opens.

Yet, unlike at the Australian Open when Rafael Nadal had beaten him in five sets, Federer had no tears.

“Today I’m OK with it,” Federer said. “I’m tired. I was tired in the other one too. Sometimes they hit you more in other ones.”

Meanwhile, Serena Williams’ doubles championship brought some closure Monday to what has been an awkward, tumultuous U. S. Open.

Time to celebrate. Time to move on. Maybe even time to make amends with the line judge she unloaded on during that ugly finish to her semifinal loss two nights ago.

“I would like to give her a big ol’ hug,” Williams said.

Williams and sister Venus teamed up for a 6-2, 6-2 victory over defending champions Cara Black and Liezel Huber to win their 10th Grand Slam doubles title, and first at Flushing Meadows since 1999. Not surprisingly, the sisters answered very few questions about doubles when it was over.

Williams had issued an apology shortly before the doubles match, saying she is “a woman of great pride, faith and integrity, and I admit when I’m wrong.”