The Swiss dropped his only set of the tournament on his way to an eighth grand slam title but ended a five-match losing sequence against the 20-year-old Spaniard.
"I would like to say it's been a great tournament for Rafael as I honestly didn't think he was going to play in the final," Federer said on Centre Court after slipping on his cream blazer.
Federer, who has won a record 48 consecutive matches on grass, said he was just relieved to get through this one.
"It's fantastic, I never thought it possible but I made it," he said. It's an incredible feeling. I was doubting myself early on in the tournament, with the draw and the expectations so to win this all over again is fantastic.
On matching Pete Sampras and Bjorn Borg's feat of winning four consecutive Wimbledon titles, the only other players to manage it in the professional era, Federer said: "They are heroes of the game.
"This is the most important tournament and to win four is out of this world. I'll come back and try for a fifth. I'm not going to quit."
