Federer, seeded fourth, beat No. 5 seed Nadal for the third time this year.
"We've had some epic matches over the years", Federer said to Nadal at the victory presentation.
Nadal would typically overpower Federer's one-handed backhand with his lefty forehand and wear him down with an endless reservoir of energy.
Squinting into the sun at the start today, Federer could not find his first serve facing two break points in the opening game.
Indian tennis star Sania Mirza and her Czech partner Barbora Strycova were stunned by unseeded giantkillers Gabriela Dabrowski of Canada and Xu Yifan from China in the women's doubles summit clash of the Miami Open here.
"I'm not 24 anymore so things have changed in a big way", said Federer, who missed Roland Garros past year.
"Maybe if you didn't see the match and just saw the score you might think it was some sort of straightforward match with a couple of breaks". That's not the full story.
Instead, he has chosen to take an eight-week break and return at the French Open, which starts on May 28.
"Always when I am playing that well, on clay it helps a little bit more for me". I have no explanation.
"It's disappointing for me that I have been trying during all my career". You will probably see me at the French.
On Twitter the reactions about Roger Federer´s win over Rafael Nadal in Miami didn´t miss.
Instead, returning to the courts after six months out due to a knee injury, he has won three of the biggest tournaments in the first quarter of the season, including an 18th grand slam at the Australian Open - his first major title since Wimbledon in 2012. On this day it went to Federer, 6-3 6-4.
For Nadal, it was a heartbreaking loss as he was fighting for the title for fifth time since 2005. But he graded the past three months favorably, viewing three runner-up finishes on hard courts as a positive. "I think that I was close", the Spaniard said.
"I'm playing enough well to fight for everything I think".
"It was an intense first set, things could have turned quickly, it could have gone either way". Then in the second it was close. In my opinion, anything could happen and it went his way, so well done for him.
Berdych actually won 91 points to Federer's 89.
"I got a few important ones", Federer said.
Roger Federer overcame long-term rival Rafael Nadal to win the Miami Open for the third time and continue his remarkable start to the season.
"I'm not 24 anymore, so things have changed in a big way", Federer told ESPN on court after his Miami win. "The body needs a break".
However, the Spaniard has distanced himself from talk about being the favourite to lift his tenth French Open crown and is focusing on upcoming tournaments in Monte Carlo, Barcelona, Madrid and Rome.
"I am at a very high level of tennis and I believe I am ready to win these titles".
"When I am not feeling this good there is no chance I will be in the finals competing with Rafa", added the 18-time Grand Slam victor after his hard court win. He said he would skip much of the approaching European clay-court season and would wait to "get on the clay" until about two weeks before the French Open, which begins on May 22.
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