The crowd sitting in the sunshine at Rome's Foro Italico watched Nadal race to victory in 69 minutes on the red clay.
Nadal, seeded fifth, dominated the first set, winning 20 of 25 points at one stage, as the Swiss second seed produced a string of unforced errors.
Federer raised his game in the second set, breaking a nine-game losing streak to go 1-3, but Nadal was in no mood to slow down. Despite being broken as he served for the match at 5-1, Nadal went on to complete his 36th win in 38 matches this year.
Nadal, 11 times a grand-slam winner, was sidelined for seven months with a knee problem and said he was delighted to be back in form.
"A very emotional and important victory for me," Nadal said. "I know Roger doesn't have his best day today. He tried to play very aggressive and he made more mistakes than what is usual for him. I think I played well I did the things well during the whole match, during the week and I'm very, very happy now I have this trophy with me. Today means really a lot."
Federer had played a number of late-night matches including his semi-final victory over Benoit Paire on Saturday (May 18) before playing Nadal in the late afternoon but the Swiss insisted the timing of the final did not make much of a difference.
"I think it was maybe more the rhythm than anything else but that was not the reason I lost today," Federer told reporters at a news conference. "The ball definitely flew a bit more through the air today, it bounced more.
"You don't hit it well it's not going to stay in so much but then Rafa has much more top spin than all the guys I've played this week so the change was a big one. I knew that coming in but I tried to play offensive and just didn't have the best day unfortunately."