The victory by the 2003, 2004 and 2006 Masters champion set up a final with another Spaniard, David Ferrer, who thrashed Andy Roddick 6-1, 6-3 in the earlier semi.
"Once I get on a roll it's hard to stop me," said Federer, who lost his opening match in Shanghai before roaring back to form against Roddick on Friday.
"I'm exactly where I wanted to be and I've got a shot at winning the title, so it's a great feeling."
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"I wish I could play like that every time against him, but it's not easy."
Roger Federer on opponent Rafael Nadal |
In an exciting first set, Federer relied heavily on his big serve, sending four aces down to recover from a 0-30 deficit in the fifth game and saving his only break point with a forehand volley in the seventh.
The Swiss player struck at the perfect moment, converting the first of three break points with a forehand down the line as Nadal served to stay in the set.
As Federer clicked into gear, Nadal was stumbling and the defending champ reeled off 14 points in a row to go two breaks up in the second.
The Spaniard finally held for 5-1 but netted a backhand to give up the match.
"It was tough at the beginning, Rafa had the upper hand," Federer said.
"But after that I got in the zone and played incredible. I wish I could play like that every time against him, but it's not easy."
No mistake tennis
Nadal was left shaking his head at Federer's display.
"I was focused on trying to contain him but he played unbelievably," Nadal said.
"He wasn't making any mistakes so it was very tough. When he's playing this way it's impossible to stop him."
Nadal is the only top-10 player with a positive head-to-head record over Federer, winning eight of their 14 matches.
He was also beaten at last year's Masters Cup by Federer, who is going for his fourth title in six appearances at the $4.45-million season finale.
"David's been the best player of the tournament," Federer said of his final opponent Ferrer.
"He's beaten unbelievable players to get this far. "It's going to be a great match tomorrow."