The six-time champion wrestled control from his compatriot and came through 4-6 7-5 7-6 (8-6) in London.
Second seed Federer will take on world number one Novak Djokovic in Sunday's final - live on BBC Two at 18:00 GMT.
Wawrinka and Federer will team up next week as Switzerland try to win the Davis Cup in France.
It looked as though the 17-time Grand Slam champion would be heading to Lille first when his friend and team-mate moved within one point of victory four times.
Wawrinka, 29, served for victory at 5-4 in the decider but might regret choosing to serve-volley on three match points, missing a makeable backhand volley on the second.
The Australian Open champion earned a fourth match point in the decisive tie-break but could not return a good serve, and Federer made him pay with a nerveless drop volley on his first match point.
"I got lucky," said a clearly relieved Federer. "Stan played better from the baseline and that usually does the job on this court. But I kept fighting.
"It's tough [on Stan] but I'm thrilled to be in another final in London."
Federer's deft winner brought an end to the longest, and by far the most entertaining, match of the week at two hours and 48 minutes, which kept the 17,000 spectators at the O2 Arena gripped throughout.
There was brilliant ball-striking from both men and controversy, as Federer argued with umpire Cedric Mourier after an over-rule in the third set which looked as if it had derailed his hopes.
Wawrinka began in spectacular fashion, breaking twice in the first set and holding off a resurgent Federer for 11 games in the second.
With a tie-break in sight, the pressure finally told and Federer broke to love thanks in part to a woeful Wawrinka smash that betrayed his nerves.
Federer appeared to be on the charge, only to be knocked off course by a dispute with umpire Mourier.
A Wawrinka backhand flew wide - later confirmed by Hawkeye - on the opening point of the final set, but Federer apparently did not hear Mourier over-rule his line judge.
It was only two points later, when Mourier announced the score was 0-40 and not 15-30, that Federer realised the situation and approached the chair.
There was nothing that could be done, however, and a flustered Federer hammered a forehand over the baseline to lose the game.
Wawrinka still faced a considerable task to keep hold of his advantage all the way to the finish line but got within a point four times, only to fall agonisingly short of only a third win over his illustrious compatriot in 17 attempts.
I can't remember the last time my palms sweat so much while watching a tennis match (2008 Wimbledon maybe). My god was this match the definition of roller-coaster!. So much back and forth.
I was literally screaming at my tv. And to top it off, my tv signal went out in the crucial moment at 6-all in the tie-break thank god for twitter!.
So many times in this match I thought it was all over for Federer but somehow with some luck (and major nerves from Wawrinka) he survived to come back one more time.
Although he's going to have to play a hell of a lot better tomorrow against Djokovic!. I just don't know if my nerves will be able to handle it.
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