Djokovic was beaten 6-2 3-6 6-4 6-1 by Nadal, who claimed the 13th singles slam of his career to move ahead of Australia's Roy Emerson (12) on the all-time list. (Agencies)
Only Pete Sampras (14) and Roger Federer (17) are above the 27-year-old Nadal on the pecking order of major champions.
"Thirteen grand slams for a guy who is 27-years-old is incredible. I mean, whatever he has achieved so far in his career is something that everybody should respect. No question about it," Djokovic said.
"I was saying before, he's definitely one of the best tennis players ever to play the game. Looking at his achievements and his age, at this moment - he still has a lot of years to play. That's all I can say," he said.
Nadal seems certain to overtake Djokovic as world number one by the end of the year.
He missed the last half of 2012, and the 2013 Australian Open, because of a knee injury, which means he has no rankings points to defend.
Following his second major triumph this year, adding the New York crown to the French Open, only another injury or inconceivable loss of form will keep him at number two.
"What can I say?" Djokovic said. "He won so much this year. I'm still number one of the world in the rankings. But year to year he's far, far ahead. He has much more chances to end up as number one,” he said.
"Look, there are still tournaments to go. So we'll see," Djokovic said.
Nadal's triumph gave him a 22-15 winning record against Djokovic and it was his sixth victory in their last seven meetings. The Serb conceded he had to find the key to reversing the trend in arguably the biggest rivalry in the men's game.
"I have to. It's part of my life. Many times you fall as an athlete. You have to learn the lesson and keep on going, keep on fighting, keep on improving," Djokovic said.
"That's what we are here for. I'm still 26, and I believe the best time for my career is about to come. As long as I believe it, the fire and the love towards the game is inside of me, as long as that's present ... I'm going to play this sport with all my heart as I did in the last 10 years," he said.
Djokovic was beaten 6-2 3-6 6-4 6-1 by Nadal, who claimed the 13th singles slam of his career to move ahead of Australia's Roy Emerson (12) on the all-time list.