Joe Rokocoko scored the only try of the match in the 10th minute after vice-captain Stirling Mortlock had kicked the Wallabies into an early lead.
Mortlock and Dan Carter then swapped penalties in a stop-start affair before the Wallabies showed signs of forcing themselves back into the must-win contest with some dogged attacking.
An enthralling second period see-sawed before the half's first points came from Carter's drop goal after winger Mark Gerrard was halted metres short of the try-line.
Gerrard then wasted another golden chance with an ill-timed fumble when he looked certain to cap a flowing move with five points as the All Blacks defence became increasingly ragged attempting to defend their narrow lead.
But New Zealand survived to win the first meeting between the old foes in Brisbane for 10 years and now look odds on to take the Tri-Nations series.
The loss sees Australia's recent unbeaten sequence in Queensland come to an end after having won all six matches at Suncorp since the rebuilt stadium was reopened in 2003.
Earlier, captain George Gregan led out the Wallabies for a record-equalling 55th time in front of an all-time high 52,498 Suncorp Stadium which included some 10,000 Kiwis.
Before kick-off, the All Blacks backed down and performed the traditional version of the haka - minus the controversial throat-slitting gesture which has dominated headlines all week.
But that did not stop them capitalising with their first chance of the match when Rokocoko beat three men to score his first All Blacks try in 11 months.
The wing scooped up an untidy pass from Jerry Collins, shook off the attention of Rocky Elsom and beat Chris Latham and Matt Giteau to the cross the line in the corner.
Latham denied Carter in the half's other major scoring opportunity when the two collided after the All Blacks five-eighth danced around the Wallabies midfield and chipped ahead into space.
But Australia finished the first half the stronger, although failed to show the try-scoring form on display in the free-flowing 49-0 demolition of South Africa a fortnight ago.
After half-time, the powerful New Zealand front row started to exert their dominance over Australia's inexperienced pack.
Wallabies tighthead Rodney Blake was having little influence on his Test return following the injury he received against England in mid-June.
And it was Rokocoko again, in acres of space, who was inches away from grabbing Carter's delightful cross-field kick.
The Wallabies nearly crossed in the corner when Mortlock cleverly played in Gerrard but the All Blacks defence swarmed all over the winger five metres short of the line.
Then, Gerrard dropped a pinpoint pass with the try-line gaping to the despair of the majority of the record-breaking Brisbane crowd.
The Tri-Nations series has five matches still to play with Australia facing South Africa in Sydney in a week's time.
The third and final Bledisloe Cup showdown, New Zealand's next clash in the series, will then be played in Auckland on August 19.