Top-ranked Nadal exploited Ferrer's inconsistent service game to take the first set and then overcame his own erratic play in the second set to win the Godo trophy at Ferrer's expense for the second straight year.
Nadal was coming off a record fifth straight Monte Carlos Masters title and improved to 24-1 in clay court finals in picking up his fourth title of the season.
The four-time defending French Open champion goes into the Rome Masters on a 25-match unbeaten run with only three defeats in his last 133 matches on clay.
Nadal and Ferrer traded breaks in the first two games before Ferrer's service game became erratic â he hit four double faults â and Nadal broke him twice more to take a 5-1 lead.
Nadal rifled an ace down the middle to take the set. Ferrer managed only four winners alongside 16 of his 41 unforced errors.
The players traded breaks to open the second set before Ferrer improved, while Nadal uncharacteristically sprayed his shots and finished with 21 unforced errors.
Tied at 5-5, Ferrer sailed a forehand wide to hand Nadal a triple-break chance. Nadal missed the first two tries but converted his sixth break point of the game when Ferrer netted.
Nadal won for the 35th time in 44 finals.