In a fractious final pushed into a third week for only the second time because of Sunday’s rain, the Spanish world number two, playing in his 16th Grand Slam final, also took his Paris record to a staggering 52 wins against just one loss.
Victory, which was achieved on a Djokovic double fault, allowed him to break the tie for six French Opens he shared with Björn Borg.
It was the 26-year-old’s 11th Grand Slam title, taking him one behind Roy Emerson, three off Pete Sampras and five away from the record of 16 held by Roger Federer.
For five-time major winner Djokovic, the Wimbledon, US Open and Australian Open champion, it was the end of his dream of emulating Don Budge (1938) and Rod Laver (1962 and 1969) by holding all the Grand Slams at once.
He was left to regret his unforced error count of 53 which undermined his challenge.
“For me it’s a real honour, this tournament is the most special and for me to have this trophy is unforgettable – it’s probably one of the greatest moments in my career,” said Nadal, who needed just 49 minutes on Monday to complete victory.
Djokovic, who had won the pair’s epic Australian Open final this year, admitted that Nadal had been the better player.
“Rafa was better. He is a great player but I hope to come back next year and do better,” said the Serb, playing in his first Roland Garros final.
After Sunday’s suspension, the players, meeting in a fourth successive Grand Slam final, resumed with Nadal leading 6-4, 6-3, 2-6, 1-2, but with Djokovic in the ascendancy and serving for a 3-1 lead in the fourth set.
But a forehand error from Djokovic, with the court at his mercy, gave Nadal a break point and the Spaniard seized it when the Serb had been left flat-footed by a net cord which allowed his opponent to push through a winner.
The set remained tight as would be expected with the pair meeting for a 33rd time.
Nadal moved to 5-4 as the umbrellas went up all around Philippe Chatrier Court and the players sat courtside to wait out a passing, heavy shower and complained to tournament referee Stefan Fransen about the slippery conditions.
Djokovic finally buckled when a monster forehand from Nadal set up championship point which he converted when the top seed tamely served up a fourth double fault.
The celebrations were ecstatic as Nadal fell to his knees and consoled Djokovic before the champion climbed into the player’s box to embrace his family.
On Sunday, Djokovic had looked down and out at one stage, even picking up a warning for destroying his courtside chair box with his racquet.
After slipping two sets down, he was also a break behind at 0-2 in the third before he reeled off eight games in succession to take the third set – the first lost by Nadal in this year’s event – and lead 2-0 in the fourth.
The first game of the fourth set had featured a gruelling 44-shot rally.
But Nadal had raged at tournament referee Stefan Fransen for having to keep playing as the court became increasingly treacherous.
As he stormed, Djokovic, who had been two sets to love down to Andreas Seppi in the fourth round, and saved four match points in his quarter-final victory over Jo-Wilfried Tsonga, seized his chance to get back into the match.
The last time a French Open men’s final failed to be completed on the last Sunday was 1973 when it was played on the Tuesday with Ilie Nastase beating Niki Pilic.
Monday finishes have become common at the US Open in New York with the last four finals taking place on the extra day while the 2001 Wimbledon final was also completed on a Monday.
Roland Garros will eventually avoid late finishes as a main court with a retractable roof is to be built in 2017.