"I'm sorry for that final but you played well," he told Federer.
"I want to thank Roger for his attitude on the court."
Federer, beaten in the French final by Nadal in the two previous years, kept his pre-match promise of playing attacking tennis, but made too many errors early on as Nadal ripped through the first set in 32 minutes.
The Swiss lifted in the second set and had a break point at 3-3 but Nadal kept his cool andthen went on to steamroll his opponent in the third, clinching the title without dropping a set.
|"I would have hoped to do better than four games but Rafael is very, very strong."|
World number one
"I would have hoped to do better than four games but Rafael is very, very strong," Federer told the crowd.
"He dominated this tournament like maybe no one before except Borg, so congratulations Rafa.
"It was still a good week. Losing in a final is never easy but I will try again next year."
Federer made a huge 35 unforced errors in the three-set match, while Nadal conceded only seven.
Nadal's 6-0 final set win was the first time that Federer had lost a set to love since the first round of the Queen's Club tournament in London in 1999, against Zimbabwean Byron Black.
It was the shortest French Open men's final in terms of games played since 1977 and the quickest final, at 108 minutes, since 1980.