The Swiss fourth seed won 6-3, 6-4, 7-6 (8/6) in just over two hours and will now face top seed Novak Djokovic for a place in Sunday's final.
Nishikori had mastered the Lausanne native over five sets in the quarterfinals at last year's US Open, but it was a far different outcome this time.
Wawrinka dominated with his serve and backhand to reach his third Grand Slam semifinal and a chance of playing in back-to-back finals at the Australian Open.
He broke Nishikori's service three times and lost serve only once, while winning 86 percent of his first-serve points.
"I am still nervous about that tiebreak, I was a bit defensive, it's never easy, you have to go for it and I'm happy to get through," Wawrinka said about blowing five match points.
"It's going to be a tough one in the semi, but I'm playing well so I am happy to be back again to be playing in the semi-final. I will watch tonight's match and then practice tomorrow."
Wawrinka set out to attack Nishikori's forehand and got a service break in the fourth game after Nishikori netted a forehand.
The Japanese superstar fought off two set points in the eighth game before Wawrinka served out for the opening set.
Nishikori again came under pressure in the second set, fighting off a break point in the third game before he was broken in the fifth by a scorching Wawrinka backhand winner.
The Japanese star saved three break points in his next service game before Wawrinka served out for a two sets to love lead.
The US Open finalist jumped out to a 2-0 lead in the third set, but the Swiss quickly broke to love with a cracking backhand cross-court winner and then levelled up.
Both players swapped breaks early in the third set before it went to a tiebreaker and Wawrinka stormed to five match points.
But he lost them all before Nishikori attempted a netted drop shot from the baseline to set up another match point.
Wawrinka made no mistake with an ace to clinch victory.
TENNIS
Nishikori win sends Wawrinka to semifinals
Defending champion Stan Wawrinka wasted five match points before sealing a straight sets win over Japanese fifth seed Kei Nishikori to reach the semifinals at the Australian Open on Wednesday.
ROGER FEDERER
Is this the end of the road for Swiss tennis legend Roger Federer?
Roger Federer is talking optimistically about returning to his "highest level" after knee surgery, but does tennis have to start adjusting to a future without the Swiss star?
The 20-time Grand Slam winner announced on Wednesday that he would be sidelined until 2021 after his second operation in a matter of months.
Federer remains upbeat, tweeting: “I plan to take the necessary time to be 100 percent ready to play at my highest level.”
In some ways 2020 is a good season to miss after the coronavirus ravaged the tennis schedule. Writing Federer off in the past has proved dangerous.
He returned from a six-month injury lay-off to claim the Australian Open in 2017, winning his eighth Wimbledon crown later that year.
But he will be 40 in 2021 and is now heading into uncharted territory.
Despite his groaning trophy cabinet, there are two factors that will motivate Federer to keep going — the risk of losing his grip on the men's Grand Slam title record and a missing Olympics singles gold medal.
Rafael Nadal has 19 majors, just one shy of Federer's mark and Djokovic has 17.
Spain's Nadal will be fancied to draw level with Federer at the French Open, rescheduled for September, while few would bet against Djokovic winning in New York weeks earlier.
In April, Federer said he was “devastated” when Wimbledon was cancelled for the first time since World War II. Last year he fell agonisingly short at the All England Club, failing to convert two championship points on his own serve against Djokovic.
The Wimbledon grass probably remains his best chance of adding to his Grand Slam collection — he has not won the US Open since 2008 and his only title at Roland Garros came in 2009.
Even though Federer has slipped from the very pinnacle of the game, he is still a major threat to Nadal and Djokovic.
'Golden' ambitions
Last year, the world number four had a 53-10 win-loss record and he reached the semi-finals at the Australian Open in January in his only tournament this year.
Federer, who is still six ATP titles short of Jimmy Connors' all-time record of 109, has one glaring omission from his CV — the Olympic title.
The Swiss won doubles gold in Beijing in 2008 with compatriot Stan Wawrinka but lost in the singles final to Andy Murray in London four years later.
The postponed Tokyo Games will almost certainly be Federer's last opportunity to complete a career “golden” Grand Slam — he will turn 40 on the day of the closing ceremony next year.
Tennis will feel the loss of the elegant Federer keenly when he walks off the court for the last time.
Djokovic and Nadal have been the dominant forces in recent years but the Swiss remains the biggest draw and last month topped Forbes' list of the world's highest-earning athletes.
His last appearance on court was in front of nearly 52,000 fans — touted by organisers as a world record for tennis — at a charity match against Nadal in Cape Town in February.
Federer is nearly always the crowd favourite wherever he plays and has proved a perfect ambassador for the sport since he won his first Grand Slam title in 2003.
He certainly expects to be back and competitive next year.
“I will be missing my fans and the tour dearly but I will look forward to seeing everyone back on tour at the start of the 2021 season,” he tweeted.
The avalanche of support from his adoring fans showed they would miss him too, but they will have to get used to a time when he is gone for good.
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