The 6-4 5-7 6-4 6-4 victory gave Djokovic three of the year's four grand slam titles with a loss to Stan Wawrinka in the French Open final his only blemish.
Although there was no way to tell how big his four-set loss to Wawrinka would be, it ended up denying the Serb a chance to join the men's calendar year grand slam club that includes just two members, Rod Laver (twice) and Don Budge.
"It's been an incredible season. Next to 2011 probably the best season of my life," said Djokovic, who won the same three grand slam titles in 2011.
"But I'm enjoying this year more than any previous one because I'm a husband and I'm a father and that makes it even more sweeter. I love this sport," he said.
It was the 10th career major for Djokovic but only his second U.S. Open.
The 28-year-old Serb had known more frustration than success on the Flushing Meadows hardcourts having previously reached the final five times and lifting the trophy just once in 2011.
It was more grand slam misery for the 34-year-old Swiss who, for the second consecutive grand slam, reached the final only to be denied an 18th title by Djokovic.
"I had a wonderful last two weeks," Federer, who has been stuck on 17 grand slam title since 2012, said after competing in his first U.S. Open final in six years.

"I'm very pleased where my game's at,” he said.
Meeting for the 42nd time the rivalry between the elegant Swiss and the dominating Djokovic has developed into one of the sporting world's best and the latest installment, perhaps fittingly, deadlocked the head-to-head series at 21-21.

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