In a controversial finish at Docklands stadium, French referee Mathieu Raynal took the ball off Australia scrumhalf Nic White (32) for time-wasting as he was poised to kick the ball clear from defence with Australia holding a three-point lead.
Gifted possession, the All Blacks spread the ball wide to Barrett who crossed at the left corner as a crowd of 53,245 at Docklands stadium gasped.
It was a bruising contest, with a slew of injuries on both sides, including both the teams' captains.
All Blacks captain Sam Cane (30) clashed heads with midfield teammate David Havili (27) in the first half and both were ruled out of the match.
"Obviously there was a lot of carnage out there, a fair few injuries," Cane said.
"To win it on the buzzer we're obviously hugely delighted. To the Aussie boys what a test match."
Barrett's cool finish secured the trans-Tasman Bledisloe Cup the All Blacks have held since 2003 with a match to spare.
In a clash featuring four yellow cards - three given to the hosts - All Blacks hooker Samisoni Taukei'aho (25) grabbed a try at the start of both halves, while flyhalf Richie Mo'unga (28) and Will Jordan (24) also crossed in a three-minute burst after the break.
The Wallabies rallied bravely with a late brace of tries by winger Andrew Kellaway (26) and Pete Samu (30) nearly brought the roof down with a stunning try assisted by Marika Koroibete (30) in the 73rd minute.
"Absolutely gutted. I actually don't know what to say," said the Wallabies stand-in captain James Slipper (33), who came off early with a calf problem.
"We just fell short there. It's probably the most gutting way to finish."
Referee Raynal's late call left home fans howling in rage after White slotted a long-range penalty for Australia.
"I'm gutted for our men because I reckon we deserved better," said coach Dave Rennie.
"It's a disappointing way to lose it.
"Of course, the clock stopped, so there was no real urgency to do that," Rennie said of the referee's decision.
"It lacks a little bit of feel for such an important moment in the game."
The win keeps the defending champion All Blacks top of the Rugby Championship table on 14 points, four ahead of Australia who grabbed a bonus point in defeat.
Argentina and South Africa, each on nine points, face off in Buenos Aires on Saturday.