By then, Federer had racked up 22 consecutive holds in the tournament for 3-all.
Meanwhile, Nadal lost his fifth Miami Open final after suffering defeats in 2005 (Federer), 2008 (Nikolay Davydenko), 2011 (Novak Djokovic) and 2014 (Novak Djokovic).
Federer failed to take advantage of five early break-point chances himself but broke in the next to last game of both sets.
Kyrgios' final risky shot backfired - a 128-mph second serve sailed long for a double fault.
The Swiss missed six months in 2016 with a knee injury before returning to action in the Australian Open and he has since won 19 of his 20 matches and comfortably leads the Race To London.
He said: "This is where it all started for us in 2004 when you were a little boy who grew into a big man and strong man". The next point was the longest of the match, and Federer ended the 19-shot rally with a forehand victor in the corner.
Rafael Nadal, of Spain, serves to Roger Federer, of Switzerland, during the men's singles final at the Miami Open tennis tournament, Sunday, April 2, 2017, in Key Biscayne, Fla. And then you hope for something else: You hope something special breaks out to cover the day in manner that makes you win by just showing up. "When you are number one and two in the world for so long, that's another thing", said Nadal with regards to their rivalry. Youre too good not to..
After all, it's Federer and Nadal.
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Rafael Nadal takes what's positive from his 6/3 6/4 loss to Roger Federer in the Miami final. "Well done. Very happy for you". 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.
The 35-year-old swept the once dominant Nadal while needing just 94 minutes to down his opponent on Sunday afternoon.
Federer, who missed the second half of previous year recovering from knee surgery, has made a rousing return to the court in 2017, winning three of the four tournaments he has contested, including the Australian Open.
Roger Federer should have been exhausted. "Ro-ger! Ro-ger!" He is a former WTA Writer of the Year and the author of numerous books, including the classic "The Courts of Babylon" and the New York Times bestseller (with Pete Sampras), "A Champion's Mind".
"Of course I'd like to thank my team as well".
"I feel like there is a mountain to climb in Rafa. I will see you next year".
"I will probably stay on hard courts. and get on the clay two weeks before the French, that's the plan for now and hopefully I will play the French and we will see how the build-up is going to go and for me that's essentially when the season really starts".