The two greatest players of their era, and possibly ever, met for a 33rd time and for the 23rd time it was Nadal who triumphed.
It is a remarkably one-sided record for two men at the top of the game, and with Federer now 32, his chances of closing the gap appear to be reducing all the time.
He has not beaten Nadal at a grand slam since the 2007 Wimbledon final and was second best throughout in a 7-6 (7/4) 6-3 6-3 defeat on Rod Laver Arena.
Nadal has never lost a set to Wawrinka, who will overtake Federer to become Swiss number one on Monday, and should he continue that record he would become the first man in the Open era to win all the grand slams at least twice.
The 27-year-old would move to 14 overall, only three adrift of Federer and level with Pete Sampras, who will present the trophy on Sunday and was among the crowd to witness Nadal's masterclass.
"I played well tonight," said the world number one. "I think I played probably my best match of the tournament. So I'm very, very happy for this great news. It's a very special moment to have the chance to be in another final."
The first set was tight but it was Nadal who had the break points, missing three before making his superiority count in the tie-break.
Nadal finally broke serve in the sixth game of the second set, and at no point did a Federer comeback look on the cards.
Nadal insisted his record against Federer was not a weapon, saying: "I went on court knowing that it's a really tough match and if I am not playing my best, I will not have the chance to win. So when I go on court, I go with doubts. But the doubts are good."
Doubts about the outcome centred on Federer's brilliant form in beating Jo-Wilfried Tsonga and Andy Murray, while Nadal was struggling with a blister on the palm of his left hand.
The Spaniard took a medical time-out after the first game of the second set to have it retaped, but he said: "The blister is good. It looks better every day. The problem is to cover that blister in the position where it is."
Walking off court a loser against Nadal was a familiar feeling for Federer, who will drop to eighth in the rankings on Monday, and he was frustrated he was not able to trouble the Spaniard more on serve.
Federer's only break points came in the fourth game of the third set, and although he did take one, it was no more than a blip for Nadal.
He said: "I think Rafa played well. He's played me this way many times.
"It was just the lack of opportunities I created for myself which put the pressure on me too frequently, instead of maybe being able to do that the other way around.
"He did a good job. Overall he was more consistent. He deserved to win tonight. He was better."
Missing out on an all-Swiss final against Wawrinka was another blow for Federer, but he will leave Australia at least knowing he is back in the grand slam mix.
Last season the chances of the 32-year-old winning another major title appeared to have gone, but with back problems seemingly behind him, a new racquet and a new part-time coach in his boyhood hero Stefan Edberg, Federer sees plenty of cause for optimism.
He said: "I wish I could have won here and given an all-Swiss final. That's something I'll regret for a long time.
"But I think this is a very good start to the season for me overall. I still feel my best tennis is only ahead of me right now."
Federer, meanwhile, was heard to complain to umpire Jake Garner about Nadal's grunting, although no action was taken.
The Swiss confirmed it was not the first time he had brought the matter up, while he also called for consistency in applying the time violation rules, with Nadal a persistent offender.
He said of the noise Nadal makes when he hits the ball: "It goes in phases. One point he does and then he doesn't. That's what I was complaining about. But it had no impact on the outcome of the match."
Nadal appeared surprised Federer had brought up the issue, and he said: "If I bothered him in any moment, he knows 100 per cent it was not because I wanted to. I never do anything on court (deliberately) to bother the opponent."