Having charged ahead on the back of a rampaging display by Fiji-born number eight Radike Samo, the Wallabies were gradually reeled in by the All Blacks as they racked up 17 unanswered points to level at 20-20 after the hour.
So often prone to being over-run late in matches by their trans-Tasman rivals, the Wallabies stood firm, however, and were given breathing space when fleet-footed fullback Kurtley Beale finished off a brilliant sweeping movement.
The hosts then withstood 20 nerve-wracking minutes of unrelenting pressure in front of 51,000 roaring fans at sold-out Lang Park to seal their first southern hemisphere title in a decade.
The relevance of the result for next month's global showpiece in New Zealand was downplayed by coaches on both sides.
"It's obviously a significant result for us. We haven't done that since 2001 so that's a baggie," Wallabies coach Robbie Deans told reporters.
"In terms of the World Cup it's irrelevant and if anything we've probably just put the bar up to that end certainly should we be fortunate enough to meet the All Blacks again.
"But we'll take some real value out of it, there's no doubt about that ... But these blokes really kept their nerve, got their hands on the ball and produced enough pressure to get the result, so that was an important step for us."
The loss, only New Zealand's second in the past 13 matches against the Wallabies, also had a sting in the tail for the All Blacks who lost number eight Kieran Read and flanker Adam Thomson to injuries in the first half.
The injuries undoubtedly played havoc with Graham Henry's plans, but the New Zealand coach slammed his players for their poor first half display.
"I think they just had more edge than us initially and we suffered because of that," the stony-faced Henry said.
"We came right in the finish but didn't do the business ... Some guys would have been disappointed in how they played, didn't play as well as they normally played and didn't play to the standard that they played to get into the side.
"Some people will be disappointed they didn't take advantage of the opportunity tonight."
The Wallabies' win was a stunning turnaround from the 30-14
trouncing the All Blacks dished out in their first Tri-Nations meeting in Auckland earlier in the month.
It was also a dream debut in the captaincy for towering lock James Horwill after a week of off-field drama.
The 26-year-old's shock appointment three weeks out from the World Cup was overshadowed by youngster James O'Connor's no-show at a team photo-shoot and function, which cost the back his place in the team and robbed his captain of one of his most valuable attacking players.
Horwill led his Queensland Reds side to victory over the All Black-laden Crusaders at Lang Park earlier in the year and it was fitting that his Reds team mates played heroic bit-parts at their home-ground.
Samo, a 35-year-old recalled for his first run-on role in seven years, launched himself into the breakdown like a human wrecking ball and gave the Wallabies a commanding lead in the 34th minute.
After fending off the wounded Thomson, the number eight bolted 60-metres to the line before fly half Quad Cooper slotted the conversion to lift the lead to 17 points at the break.
Cooper had earlier opened the scoring, slotting a penalty in the third minute before Will Genia went over for a try in the 12th minute after the television match official incorrectly awarded the Australians an attacking five-metre scrum.
It was a different All Blacks side that emerged after the break as they controlled possession and built phases, with Dan Carter adding his second penalty before Conrad Smith and Ma'a Nonu each scored tries to level the score at 20-20.
Outside centre Smith's try was just reward for patience and hard work after the All Blacks mounted a 28-phase drive that broke the Wallabies defence and stole back the momentum.
Nonu's 59th minute try raised the temperature to boiling point, prompting Horwill to call his team mates in for a huddle.
The lock later joked that he could not remember what he had told his troops but the message seemed to sink in as Beale crossed a minute later for a try that lifted the roof.
More drama was to come as Cooper shanked two gettable penalties, but the Wallabies slammed the door shut with iron-willed defence to clinch their third Tri-Nations trophy.