Nadal's win was in a powerful performance that showed he has quickly returned to near his best after a knee injury.
Ferrer was a three-time defending champion and had won 19 straight matches in this event, but he could find no answer to Nadal, losing to his Spanish compatriot.
Nadal surprised himself with the one-sided victory.
"I did not do anything wrong today, I had a great match, almost perfect," Nadal said. "I would have never imagined playing at the level that I played today, I'm leaving happy and surprised.
"I played a great match against one of the top players in the world, a specialist in clay who did not look like himself out there, he had a bad day."
The women's final was similarly one-sided with Italy's Sara Errani beating Carla Suarez-Navarro of Spain 6-0, 6-4.
Nadal missed seven months with a left knee injury before making his comeback in the Latin American clay court season.
He has played three tournaments: making the final but losing to Horacio Zeballos in Chile, taking out the Brazil Open by beating David Nalbandian and cruising past Ferrer for his 38th clay title. Seven of those 38 have been against Ferrer.
Nadal is ready to test his knee on the more jarring hard-court surface at the upcoming Indian Wells tournament after an exhibition appearance at New York's Madison Square Garden.
"Indian Wells is one of my favorite tournaments and I want to keep competing because the knee is holding up and my heart says that I can do it, and compete is what I want to do now," Nadal said. "Those seven months are in the past, hopefully forever. I played like that did not happened, but it did happen."
The 11-time major champion broke Ferrer five times in eight opportunities, winning 58 percent of his return points. He improved his record against Ferrer to 17-4.
Ferrer had defended titles already this year at Auckland and Buenos Aires, but was not able to make it four straight Mexican Opens.