Djokovic, the world number one, began their 54th encounter in appalling fashion. The Serb lost his opening service game and the Spaniard held to take a 2-0 lead.
Seemingly affected by his three hour semi-final against Diego Schwartzmann on Saturday, Djokovic failed to muster a response and lost his second service game to trail 0-3. His fortunes did not improve.
Nadal romped away with the set to register the first 6-0 in all of their meetings.
Djokovic finally got on the board in the second set and he showed guts at 3-3 to recover from 0-40 to go 4-3 ahead. He also saved a break point when serving at 4-4.
After flirting with oblivion for most of the set, Djokovic pounced to take it 6-4 and level at one set apiece after nearly two hours of one-way traffic.
But parity did not last long.
Djokovic dropped his opening service game of the decider and vented his frustration on his racquet, smashing it three times at the back of the court.
Nadal, unruffled by the theatrics, held to take a 2-0 lead and had a break point for a 3-0 advantage.
But Djokovic saved it with a sumptuous backhand winner down the line. He won the next two points to halve the deficit and maintain the intrigue.
But the tension did not last. Nadal reeled off the next four games to take the claim the set 6-1 and the match in just under two and a half hours.
It was his first title of the year and a record 34th crown at a Masters event which are considered just below the Grand Slam tournaments in terms of prestige.
"Winning a title is important," said Nadal. "But it is important to feel healthy and competitive.
"You can win and you can lose but as long as you have your physique, that's crucial."