Conrad Smith dives over for his second-half try
Australia will head into next Saturday's Test against England on the back of another defeat after they lost 32-19 to New Zealand in Toyko.
The Wallabies, who have only won once this year, had led 16-13 at the break with Peter Hynes scoring a try.
But the All Blacks, who face Wales next week, hit back and tries from Conrad Smith as well as Dan Carter's 22-point haul sealed the win.
The win gives New Zealand a 4-0 clean sweep in this year's Bledisloe Cup.
New Zealand have now won their last seven games against Australia.
"It's pleasing to be 4-0 against the Wallabies this year. It's not a personal thing, it's a win-loss thing," said coach Graham Henry.
"And it's great to have momentum going into the European tour. It's always better when you travel 12 and half hours on a plane with a win under your belt."
The Wallabies did produce a stronger performance than their last clash against the All Blacks, which they lost 33-6, but they were undone by handling errors and a lack of a cutting edge.
New Zealand scored the first try through wing Sitiveni Sivivatu after a fine build-up with flanker Richie McCaw heavily involved.
Sivivatu was then sin-binned for a dangerous tackle on an airborne Adam Ashley-Cooper and Australia took advantage with Hynes awarded a controversial try when referee Mark Lawrence became frustrated at the delay in the decision-making of a television match official.
Smith put the All Blacks back in front five minutes into the second half when he stepped through the Australia defence after a charge by Cory Jane.
Carter's kicking saw his side home and his fourth of six penalties brought up his 200th point in Tests against Australia.
Both New Zealand and Australia now travel to Europe for their autumn internationals.
New Zealand play Wales on 7 November and then take on Italy, England and France on successive weekends.
Australia meanwhile, who will be without vice captain Berrick Barnes for the trip because of injury, have a Grand Slam tour against England, Ireland, Scotland and then Wales on 28 November.
New Zealand: Muliaina; Jane, C Smith, Nonu, Sivivatu; Carter, Cowan; Woodcock, Hore, Tialata, Thorn, Donnelly, Thomson, McCaw, So'oialo.
Replacements: Afoa for Tialata (46), Read for So'oialo (54).
Not Used: Flynn, Eaton, Leonard, Donald, Ellison.
Sin Bin: Sivivatu (32).
Australia: O'Connor; Hynes, Cross, Ashley-Cooper, Ioane; Giteau, Genia; Robinson, Moore, Alexander, Horwill, Chisholm, Elsom, Pocock, Palu.
Replacements: Polota-Nau for Moore (49), Mumm for Chisholm (50), Smith for Palu (54).
Not Used: Dunning, Burgess, Mitchell, Cooper.