Nadal made history in the opening set by cruising to a 6-0 victory, the first time it had been done in a clash between the two megastars.
Djokovic hit back by winning the second-set 6-4.
The Serbian then lost his temper at the start of the third set after he was broken by Nadal, and proceeded to make a mess of his racket.
Before the clash, Djokovic snubbed Roger Federer by naming Nadal as his ‘greatest rival’ in the sport.
“He keeps on showing to the world why he’s one of the biggest legends of tennis history,” Djokovic said of his next opponent Nadal to the official ATP website.
“I have the greatest respect for him. He’s my greatest rival of all time, for sure.
“Every time we get to play each other, it’s a thrill.
“It’s the ultimate challenge.”
Before the match Nadal sent out a warning to his fellow French Open hopefuls, by commenting on his recent form.
He said: “The main thing is I am playing better.
“If I play better, I know I’m going to have chances to be in finals and to win semi-final matches.
“If you are not playing well, [beating] the best players of the world is much more difficult.
“I have margin to keep improving. But, I am doing the right steps to be there.”
Former professional Greg Rusedski has backed Nadal if the Spaniard is to meet either Djokovic or Federer at Rolland Garros.
“The greatest fighter we’ve ever known in our sport so he is going to find a way to get back to his best,” Rusedski said on Amazon Prime.