Djokovic, 26, beat the defending champion and world number one in two hours and 19 minutes, ahead of the French Open which begins on Sunday.
It is the first time since 2004 that the Spaniard, who was beaten in the quarter-finals in Monte Carlo and Barcelona, has lost more than two matches on clay in a season.
“I played three very tough matches this week and it was very hard mentally, as well as physically,” said Nadal, who admitted being a little tired.
“Winning a final of a great tournament with Rafa on clay is definitely a confidence booster and the ultimate challenge,” said the triumphant Djokovic.
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