Nadal shattered Federer's dream of a record sixth successive Wimbledon title with a 6-4, 6-4, 6-7 (5/7), 6-7 (8/10), 9-7 triumph in the longest final in the tournament's history to add a first title here to his four French Opens.
"He's still the number one. He's still the best. He's still the five-time champion here. Right now I have just one," said Nadal, the first Spanish men's winner since Manolo Santana in 1966.
Despite losing what will comfortably be regarded as the greatest final in Grand Slam history, Federer will remain the world number one for the 231st week when the new rankings are released today.
Nadal will stay at number two for the 155th week.
But after his ruthless demolition of Federer four weeks ago in the French Open final to claim a fourth successive Paris crown, and becoming only the third man to win Roland Garros and Wimbledon in the same year, it is the 22-year-old Spaniard who is now widely seen as the world's top player.
He ended Federer's 65-match, six-year winning streak on grass, a significant psychological blow with the Swiss still without a French Open title to add to his 12 Grand Slam trophy collection.
"It's more of a surprise to win here than the French," admitted Nadal.
"It's my most emotional win and probably the best."