Both sides scored three tries, but with a damaging penalty count, Australia allowed Dan Carter too many shots at goal and he delivered.
The Wallabies needed to beat the All Blacks to stay in the hunt for the trophy and were in good shape when they took a 20-11 lead into the half-time interval.
But the hosts dominated the second half as Australia struggled under the weight of a monstrous All Blacks scrum and a mounting penalty count, and a late surge was not enough to get them over the line.
An intercept try to Lote Tuqiri and a late five-pointer to Rocky Elsom allowed the Wallabies a sniff of victory in the first half, with the All Blacks struggling to find rhythm.
New Zealand had been controlling the play with several significant breaks, but too often final passes were forward and handling mistakes cost them when opportunities were provided.
It was in one such move when flanker Jerry Collins was in the backline that a long pass floated towards wing Doug Howlett fell into Tuqiri's hands and with only an injured prop Carl Hayman between him and the line it was no race.
Hayman was forced to leave the field and was replaced by Greg Somerville.
However, the All Blacks fought back and from their first driving maul at the line, lock Jason Eaton leapt over the maul and scored.
Moments later, a solid Australian attack produced a try when Elsom was ruled to have grounded the ball over the line before losing it.
Carter did not have to wait long to get the All Blacks back in touch, booting two quick penalties to get back to within three points.
New Zealand were camped in Australia's half for much of the second half and when lock Chris Jack raced in for a try in the 63rd minute, the home side was back in front.
Australia's woes continued five minutes later when Luke McAlister picked up the scraps of a damaging Carter tackle and bolted 45 metres to score and give the All Blacks a 29-20 lead.
The Wallabies hit back late in the half when Tuqiri snared his second try, but it proved too little too late as New Zealand added to their trophy cabinet.