The Spaniard, who ended the season without a Grand Slam title for the first time since 2004, congratulated the top-ranking Serbian for his "amazing" run culminating in last month's US Open title, his third major of the year.
"The mental strength and the level of tennis is difficult to equal," Nadal, 29, said sitting next to Djokovic at a press conference in the Thai capital.
"I texted him after the US Open, but I want to say today in a public way, it's amazing the way he's playing during the whole season."
The 14-time major winner crashed to his earliest exit in New York in 10 years in September, beaten by Italian Fabio Fognini in the third round after being two sets up, with questions raised over his fitness.
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The former world number one, now ranked seventh, faced similar scrutiny after quarter-final exits at the Australian and French Opens and a second-round loss at Wimbledon.
In September Djokovic, 28, seized his 10th Grand Slam title and now stands just seven behind the record of Roger Federer, who he has defeated in the US Open final.