However, fan favourite Federer broke at a crucial moment in the final set to go into a 4-2 lead, and the 35-year-old served out for victory to secure a 7-5 6-3 1-6 4-6 6-3 win.
Federer is eyeing an historic 18th Grand Slam title – and his first since 2012.
The most successful male tennis player in history will face the winner of Friday’s semi-final between Rafael Nadal and Grigor Dimitrov.
The Swiss will become the oldest men's grand slam finalist since Ken Rosewall featured in the US Open in 1974 at the age of 39.
"It's all real, I never thought in my wildest dreams I would come this far in Australia," a glowing Federer said in his courtside interview, having come to Australia with no expectations after six months out of the game.
"I've got a couple of days off. It's beautiful. I'm probably (Nadal's) number one fan.
"I'm happy we've had some epic battles over the years."
Highlights as Federer reaches his sixth Australian Open final
Federer unusually took a medical timeout in his three-hour, five-minute battle with Wawrinka, saying he had been carrying an upper leg injury.
He said he was not worried about it and nothing was going to stop him from taking to the court and fighting it out for a fifth Australian Open crown on Rod Laver Arena on Sunday.
"I'll leave it all out here in Australia and if I can't walk for another five months, that's okay. I'll give it my best shot," he said.
"It feels amazing. I never, ever in my wildest dreams thought I would come this far in Australia. I have a couple of days off. It's beautiful, I'm so happy."