Nadal fell to 0-5 in Key Biscayne finals, including in 2005 against Federer.
Nadal then responded by forcing Federer back to deuce and held a break point, but netted a stretching forehand.
That sequence typified today's Miami Open final. He has now won his last four meetings between the pair.
"It was a very intense first set", Federer said. "He was playing big tennis, stepping in doing all the right things..." Unlike the first set, where the service was always threatened by the subtractor, in the following there was a spice of truce until the seventh game.
They met for the first time there 13 years ago. "It's so crucial against a great return player like him to always protect your serve". Nadal turns 31 in June, and only a fortnight ago, Federer, age 35, became the oldest victor of a Master title in Indian Wells.
Federer will be rising to No. 4 on the ATP rankings, adding the Miami title to his Indian Wells and Australian Open trophies.
The Spaniard was playing in his fifth Miami final but remains without a win in the Masters series event.
It gave him the chance to serve out the win and Nadal went long moments later, ensuring Federer's stellar start to the year continued.
Its disappointing for me that I am trying during all my career, Nadal told the crowd with a smile during the trophy ceremony. I already played three finals this year, losing three times with a player that didn't lose a match - only one match that he never would lose in normal conditions in Dubai and that's it.
"What a start to the year". Whatever it is, Federer has regained shades of his invincible best.
I'm not 24 anymore so things have to change in a big way and I probably won't play any clay court events except the French.
Federer saved two match points in his quarterfinal win over Tomas Berdych. I need to work hard to be ready for that. Indeed, their rivalry had begun in this very tournament the year before. Rafael Nadal could not do it on this Sunday in the final of the Miami Open.
Nadal was so eager to reach the Key Biscayne final that he ran out of his shoe. This time it was the Miami Open, and Sunday's score was a forceful 6-3, 6-4.
He did not. The match was taut as violin strings, a well-played exchange of held serves interrupted only by Federer breaking Nadal in the eighth game of the first set and ninth game of the second, just when you figured tiebreakers might be looming.
In a crackling rally, rivals collaborated to hit three lines.
Nadal had been dominant in nearly all facets of the game coming into the final, but his level dropped immensely in the final, only winning 66 percent of his first serve points and 50 percent of his second serves.
In the fourth game it was he who had two break opportunities.
He exuded control throughout, breaking at 4-4 in the second and serving out. He claimed two of nine break points, while turning aside all four he faced.
Then, in late January, Federer tweaked his knee while running a bath for his children the day after his Australian Open semifinal loss to Novak Djokovic.
But it was Fed who broke first, a good sign for the Swiss.