Wawrinka’s victory sealed second place behind group winner Rafael Nadal and the world number four will play six-time champion Federer in a rematch of last year’s stormy semi-final at the prestigious season-ending event at London’s O2 Arena.
Federer won that meeting in three sets after saving four match points, but the game is mostly remembered for reports of a heated post-match row between the players which was allegedly sparked by Federer’s wife Mirka heckling Wawrinka and calling him a “crybaby”.
“I’m excited to be back for the semi-finals. It was tough battle,” Wawrinka said.
“I played a crazy match against Roger in the semi-finals last year. I will try and go and get some rest and be ready.”
Defending champion Novak Djokovic faces Nadal in the other semi-final earlier on Saturday.
Nadal leads Djokovic 23-22 in their career head to head, while Federer has won 17 of his 20 meetings with Wawrinka.
Wawrinka’s progress to the last four for the third successive year denied Murray the chance to win the tournament for the first time and also left the British star uncertain if he will finish the year-end rankings in second place for the first time.
He will be overhauled by Federer if the world number three wins the Tour Finals.
But, having made it clear that his main priority for the rest of the season was helping Great Britain win the Davis Cup for the first time since 1936, Murray is now free to concentrate on next week’s final against Belgium in Ghent.
Wawrinka has enjoyed a remarkable late-career rise, winning two Grand Slam titles including this year’s French Open, and this was another masterful display from the 30-year-old.
Forced to stave off two break points in the third game, Wawrinka weathered Murray’s early storm and overpowered him with some ferocious groundstrokes to secure the first break in the eighth game.
Murray responded by frustrating Wawrinka with some inspired defence before unleashing a blistering winner to break back when the Swiss served for the set.
That defiant display from Murray prompted Wawrinka to fling his racquet in disgust, but the Swiss star would end the set with a happier expression as he recovered from 4-2 down to take the tie-break.
Now it was Murray’s turn to start showing his frustrations and his angst only increased when he carelessly dropped his serve in the first game of the second set.
Wawrinka pressed home his advantage with another break for a 5-2 lead before faltering when Murray got one of the breaks back.
That set the stage for a thrilling final game, with Wawrinka saving two break points before finally sealing the win.
Earlier on Friday, Nadal battled to his third successive win at the Tour Finals, but his marathon 6-7 (2/7), 6-3, 6-4 victory over David Ferrer might prove a significant blow to his chances of defeating Djokovic.
Despite having already booked his place in the last four, Nadal refused to conserve his energy in a meaningless match against his fellow Spaniard that came just 24 hours before his clash with world number one Djokovic.
While Djokovic rested after completing his group campaign on Thursday, Nadal slugged it out with Ferrer in a draining baseline battle that lasted two hours and 37 minutes.
It will take a remarkably quick recovery from Nadal if he is to end Djokovic’s bid for a record fourth successive Tour Finals title.
Nadal is aiming to join Andre Agassi as the only men to win all four Grand Slam titles, a Olympic singles gold medal, the Davis Cup and the Tour Finals.
“Maybe I will be tired, but I’m not worried about it,” Nadal said.
“Let’s see what’s going to happen against Novak.”