Since returning from his six month injury lay-off, the 35-year-old Federer has also won the Australian Open and Indian Wells and he heads into the clay season as, once again, the dominant presence on the ATP Tour.
Federer has beaten Nadal in all of those events this year and has now won his last four meetings between the pair.
“It's been a fabulous couple of weeks,” said Federer after his victory.
The Spaniard was playing in his fifth Miami final but remains without a win in the Masters series event.
The first set was a tight affair with both players having their opportunities to break. But it was not until the eighth game and 10th break point of the set that one of them was able to get ahead.
Nadal could only find the net from a Federer backhand and the Swiss grabbed a 5-3 lead and held the next game to secure the first set.
Federer pinpointed his saving of break points in the first game and at 3-3 as crucial moments in the contest.
“It was totally key,” Federer said. “He looked good from the get-go. He was playing big tennis, stepping in and doing all the right things.
“A bit more luck on his side and the wrong decisions by me at that moment and it could have turned very quickly. It was a very intense first set.”
There has always been a marked contrast between Federer and Nadal's differing styles and with time it has become further accentuated.
Nadal was working hard in the 28C afternoon heat, thrusting himself into his shots while the elegant Federer's poise appeared almost casual.
The second set took an almost identical path, albeit with fewer openings to break for both players until Federer again pounced, to grab a 5-4 lead when Nadal went long returning a fine backhand.
Federer said he will now take a nearly two-month break from the sport before returning for the French Open in late May.
“I'm not 24 any more so things have changed in a big way and I probably won't play any clay court event except the French. That is what it is going to look like, I need rest, my body needs healing, I need time as well to prepare, you will probably see me at the French again,” he told ESPN in an on-court interview.
“I want to stay healthy and enjoy myself. Because when I am healthy and feeling good, I can produce tennis like this, when I am not feeling this good there is no chance I will be in the finals competing with Rafa.
“That is why this break coming now in the clay court season and focusing everything now on the French, the grass and then the hard courts after that is going to be the key for me,” he added.