Nadal claimed his 13th Grand Slam title after a battle that went beyond the three-hour mark at Flushing Meadows, condemning Djokovic to a second successive defeat in the US Open final.
The Serb told BBC Sport: "Obviously I want to congratulate Rafa and his team. He was too good, he definitely deserved to win this match and the trophy.
"Obviously, it's disappointing to lose a match like this. Again, it was a huge privilege and an honour to fight for this trophy.
"I will definitely be coming back next year. Thank you guys for supporting."
Djokovic reached the final of three Grand Slams this season, with his only success in 2013 coming at the Australian Open in January.