McKenzie had been dealing with an investigation into utility back Kurtley Beale's off-field conduct, amid reports about discord within the Wallabies squad and increasing speculation in the last two weeks that the coaching job was on the line.
In a muted news conference after the 29-28 Bledisloe Cup loss to the All Blacks on Saturday night, McKenzie said he'd made up his mind well before the game that it would be his last in charge.
"I resigned this morning at 10 o'clock," McKenzie said, delaying his statement until skipper Michael Hooper had left the room. "I've been a very proud contributor to Australian rugby, but I feel at this point ... there's a bunch of reasons. The intention was win, lose or draw, I was going to announce that resignation tonight."
McKenzie waited until after the match to inform the team, and none of the players were made available to comment.
"I didn't actually advise the team or any of the members of staff, so I've just done that," McKenzie said. "I'm not going to go into the detail — you guys can work that out.
"The easiest way for me is to exit stage left and I'll leave you guys to ponder, speculate and I'll write a chapter in my book and then you'll know all about it."
All Blacks coach Steve Hansen said the decision was a reflection of the challenges facing top-flight coaches.
"It's quite sad. I'm not sure if you know how hard it is to coach an international side. When things are going really good, it's still bloody tough," he said. "So sad to hear that. We take no joy out of it at all, to be quite frank. Just wish him all the best."
McKenzie had coaching success at provincial level, helping New South Wales to the Super Rugby final in 2008 — despite being told earlier in the season that his contract wouldn't be renewed — and, after a stint in Europe, returning to Australia and helping lift the Queensland Reds out of the doldrums to a Super Rugby title in 2011.
The World Cup-winning prop was appointed Wallabies coach last August, only days after Robbie Deans — the first foreigner hired as head coach of Australia's top team — was fired. McKenzie guided the Wallabies in 22 tests for 11 wins, a draw and 10 losses — that span including a stretch of seven consecutive wins.
Australian Rugby Union chief executive Bill Pulver blamed media critics for McKenzie's sudden departure, describing recent reporting as unfounded and unwarranted and saying "we lost a good man tonight."
"I think Australia has lost a great coach and a wonderful bloke and it's very disappointing we have lost a man like him," Pulver said. "In essence, Ewen said he was going to struggle to retain the level of support he needs from the playing group and, in my view, because of the character assassination he's suffered in the last two weeks.
"The attack on Ewen was relentless and essentially left him with the view it set him too far back to be an effective rugby coach."
McKenzie has been increasingly drawn into a disciplinary process involving Beale, who is alleged to have circulated offensive text messages about the team's business manager Di Patston.
Patston was involved in an argument with Beale during a team flight from South Africa to Argentina earlier this month. She has since resigned and Beale has been suspended, pending the disciplinary hearing this week.
McKenzie was forced at a news conference last week to deny he has been in an intimate relationship with Patston. Team members, including Hooper, had expressed qualified support for McKenzie in the face of media reports the coach had lost the players' confidence, but there were persistent rumours of fractures in the squad.
Finally, it got too much for the 49-year-old McKenzie. It didn't help his mood when a spectator, wearing a gold Wallabies jersey and cap, threw a full plastic cup of beer toward the Australian coach late in the game and was kicked out of the stadium.
Pulver, whose position is also under a cloud, said he'd assembled a taskforce including two-time World Cup winner John Eales, Michael Hawker and Paul McLean to try to find a replacement for McKenzie before the squad leaves for Europe on Friday.
Former South Africa coach Jake White is a contender, having narrowly missed out on the job when McKenzie was appointed last year because the ARU preferred a home-grown coach at the time. Michael Cheika, who guided the New South Wales Waratahs to the Super Rugby title this season, is being tipped locally as a key candidate.