The 13-time champion had a set point in the third set but could not convert and as he tired in the fourth, Djokovic pulled away to set up a final against Stefanos Tsitsipas.
Nadal philosophical in defeat
Defending champion suffers just his third loss at Roland-Garros
“No doubt he deserved to win,” said Nadal, who beat Djokovic in last year's final, and was targeting a record 21st major this fortnight that would have seen him surge ahead of Federer and the Serb.
“Probably was not my best day out there. Even if I [fought] and I put a lot of effort [in], the position on the shots has not been that effective tonight. “Against a player like him that takes the ball early, you are not able to take him out of his positions, then is very difficult.”
Nadal rued his missed opportunity in the third set, when he held a set point on the Djokovic serve, only for the Serb to produce a brilliant tiebreak.
“Even like this, I had the big chance with set point, 6-5, second serve,” he said. “Anything could happen in that moment. Then I make a double-fault, easy volley in the tiebreak.”
“It's true that [there] have been crazy points out there. The fatigue is there, too.
"These kind of mistakes can happen. But if you want to win, you can't make these mistakes. So that's it. Well done for him. Have been a good fight out there. I try my best, and today was not my day."
Having won the title a record 13 times, Nadal said losing for only the third time was not the end of the world. His record at Roland-Garros remains a staggering 105-3.
"My opportunities to win here are not eternal,” he told the Spanish press. “In our sport, you must admit both victory and defeat. I do know that I can't win the tournament 15, 18, 20 times. It's not a disaster at all.
"I'm sad, I lost at the most important tournament of the year for me. But it's just a defeat on a tennis court you know, and tomorrow I'll be at home with my family. That's OK.”
Nadal admitted that the slightly cooler conditions of the evening had played their part in allowing Djokovic to take control.
“Is true that probably the conditions were a little bit slower later on,” explained the 35-year-old. “We had been playing with very warm and high bounces. During the night the situation goes a little bit the other way, so it bounces a little bit less. The ball gets less topspin. That's more favourable for him.
“Doesn't matter. That's tennis. The player who gets used to the conditions better is the player who deserves to win."
Nadal said he had not decided what he would do next ahead of Wimbledon, which starts on June 28.
"I have to rest a little, physically, mentally as well, and then I'll tell what is my schedule,” he said.