The 20-year-old Spaniard extended his record-winning streak on clay to 60 matches with the 100th victory of his career on the surface, as he remains unbeaten at Roland Garros since winning on his debut last year.
After overcoming initial nerves in the first set, the world number two hammered home his dominance claiming his sixth win in seven meetings with 24-year-old Federer.
“It was a very difficult match. Roger played much better in the first set but after that, the match opened up,” said Nadal.
“It’s incredible. I think I prefer this year because it’s harder to defend a title.”
Federer said: “He deserved it because he played better. He got back into the match well and he finished off well.”
The loss ended Federer’s bid for his first French Open title and a win which would have made him just the third man to hold all four Grand Slam titles at the same time.
The Wimbledon, US Open and Australian Open champion would have become the first man to achieve the feat since Rod Laver in 1969.
Competing in just his first Paris final, Federer said: “It nearly worked this year. Last year I was in the semi-final so maybe next year it will happen. That seems to be how my career goes.”
In the meantime, Justine Henin-Hardenne refuses to believe she will ever eclipse the standards set by her idol Steffi Graf.
The Belgian outclassed eighth-seeded Russian Svetlana Kuznetsova 6-4, 6-4 in the final of the French Open to clinch her third title in four years.
The victory saw Henin-Hardenne become the eighth woman to have won the French Open three times or more – joining a list which includes Graf as well as Chris Evert, Monica Seles and Arantxa Sanchez-Vicario.
But the 24-year-old, who has always claimed a great admiration for Graf, is clearly uncomfortable with the comparison with the German great.
“It’s pretty amazing what she has achieved,” said Henin-Hardenne, who has now won a total of five grand slams after also prevailing in the 2003 US Open and the 2004 Australian Open.
“Steffi won here six times, she was a real champion. Seles and Sanchez-Vicario won three times and now there is me. It’s amazing for me to be with all those names.”
Henin-Hardenne, who was seeded fifth, played down her latest success.
“It’s only my fifth grand slam (title),” she added. “I will never be like these players.
“Some of them did things that cannot be repeated, they were the greatest champions and I would not even dream of comparing myself to them.
“It’s incredible winning so many grand slams, I feel inspired by them.