The mid-afternoon clash was not one of the most memorable in a 32-match series between them as Federer faded away in the second set to hand Nadal his first victory over the Swiss on an indoor court.
Nadal was thrashed 6-3 6-0 by a rampant Federer at the o2 Arena two years ago but on Sunday his muscular game proved too much for the Swiss who had battled for more than two hours to beat Juan Martin Del Potro on Saturday.
Federer had his chances, notably when he had break points midway through the opening set, but after levelling at 5-5 by breaking Nadal's serve for the only time he never really looked like upsetting the world number one.
"In the first set, he played very well. He was closer than me to have the break. Until 4-4 he was playing better than me," Nadal, who is one win away from filling in the only blank on his CV, told reporters.
The year could have a grand finale with the two dominant players in the world meeting on Monday, although defending champion and world number two Novak Djokovic still had to get past Stansilas Wawrinka in the second semi-final later on Sunday.
Federer's only real chance to stamp his authority on Nadal came in the sixth game.
On break point he was faced with a short ball on his forehand side but the shot that has won him so many titles misfired and he flew the ball over the baseline.
"I went for it when I had a chance for a breakpoint in the first set. Maybe I shouldn't have, but I did. No regrets there, I guess," Federer told reporters.
"I just struggled to stay consistent enough throughout the match, and that's why he deserved to win. He was better today."
Federer offered hope to his fans when Nadal served for the first set, winning a scintillating baseline exchange at 15-30 with a sweetly-timed forehand winner.
Federer then roared and clenched his fist as Nadal ballooned a forehand out to hand Federer the break back.
Just when it looked as though Nadal might be wavering, however, Federer served a double fault in the next game and Nadal then put away a forehand winner on his way to a break that was to prove decisive.
Nadal made no mistake at 6-5, winning four straight points to put one foot in the final.
When a Federer forehand nose-dived into the net on break point at 2-2 the belief seemed to drain out of the 32-year-old and the end came quickly as Nadal extended his career record over the 17-times grand slam champion to 22-10.
"It's the perfect way to finish one of the best seasons of my career to have the chance to win a title I've never won," Nadal, who has won everything in the sport apart from the season-ending tournament, said on court.
(Editing by Ed Osmond and Justin Palmer)
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