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The eighth seed triumphed after a pulsating five-set quarter-final which ran for exactly four hours and finished 2-6, 6-4, 6-2, 3-6, 9-7 when Djokovic volleyed out on the first match point.
It was a personal triumph for Wawrinka, 28, who took Djokovic the distance in last year's fourth round and was also denied by the Serb in another five-setter at the US Open.
Wawrinka's win halted Djokovic's 25-match winning streak at the Australian Open, which stretched back to 2011 and included 2012's record, six-hour final against Rafael Nadal.
It also snapped the six-time Grand Slam champion's sequence of 14 straight major semi-finals, and broke a 28-match unbeaten run dating back to the US Open final in September.
"Last year (at the Australian Open) I didn't finish it and it was really tough. But this year I came back, it's a new year and I was feeling really good," Wawrinka said.
"I tried everything, he's an amazing champion... I'm really, really, really, really happy."
Wawrinka, who was cramping by the end and headed straight for an ice bath, goes into his second Grand Slam semi-final where he will face Tomas Berdych after the Czech ousted third seed David Ferrer.
Li Na blazed past Flavia Pennetta to set up a last-four clash with emerging teen star Eugenie Bouchard, 19, who beat former world number one Ana Ivanovic.
But the earlier results were eclipsed by Wawrinka's great upset which ensures that a player from outside of the men's "Big Four" will contest the Melbourne final.
Djokovic bombed through the first set in just over half-an-hour but he stumbled in the second, and looked increasingly tight in the third, as Wawrinka took a two-sets-to-one lead.
The champion was tottering but just when he looked to be heading out against the increasingly confident Swiss, he broke for 5-3 in the fourth set, letting out a mighty yell to the heavens.
He sealed the set with an ace to take it into a fifth, where they exchanged early breaks and Wawrinka staved off another break point at 2-1 down with a titanic, 31-shot rally.
The decider stretched on until the 16th game when a Djokovic error gave Wawrinka a match point. And as the clock ticked over to four hours, the Serb's long reign crumbled when he put a volley out.
"He took his opportunities. He deserved this win today. I congratulate him absolutely. There is nothing I can say," Djokovic said.
"You know, I gave it my best. I gave it all. I tried to come out as the winner. I tried to fight till the last point as I did in a very similar match we did last year fourth round, same court, but it wasn't to be this time."
Earlier, China's Li became favourite to reach the women's final as she pummelled winners past Pennetta in the 6-2, 6-2 victory.
Li, seeking her second Grand Slam title, is peaking at the right time, with the 67-minute mauling coming after she smashed past Ekaterina Makarova in less than an hour on Sunday.
Li, 31, is gunning to reach her third Melbourne final but she faces a new challenge from 19-year-old Bouchard, who announced herself on the world stage by ousting Ivanovic.
Despite a gulf in experience and rankings, the Canadian world number 31, aggressively took the fight to former world number one Ivanovic, now ranked 14th.
Even after going a set down, she kept the pressure on the injury-affected 2008 French Open champion and won 5-7, 7-5, 6-2 to reach the Australian semi-final at her first attempt.
Bouchard's instant success in Melbourne contrasts with Berdych, who finally reached the last four at his 11th attempt, and celebrated his first-ever win at Rod Laver Arena, the centre court.
The 28-year-old seventh seed was never headed against Ferrer but he had to fight hard to prevent a comeback by the tenacious world number three, winning 6-1, 6-4, 2-6, 6-4 in just over three hours.
Results from the Australian Open on Tuesday (x denotes seeding):
Men's singles
Quarter-finals
Tomas Berdych (CZE x7) bt David Ferrer (ESP x3) 6-1, 6-4, 2-6, 6-4
Stanislas Wawrinka (SUI x8) bt Novak Djokovic (SRB x2) 2-6, 6-4, 6-2, 3-6, 9-7
Women's singles
Quarter-finals
Li Na (CHN x4) bt Flavia Pennetta (ITA x28) 6-2, 6-2
Eugenie Bouchard (CAN x30) bt Ana Ivanovic (SRB x14) 5-7, 7-5, 6-2
