The victory also ensured the Bledisloe Cup, the annual trophy contested by the trans-Tasman nations, will stay in New Zealand for a 21st year in succession.
"Very proud of the boys tonight," said All Blacks captain Ardie Savea.
"The Wallabies came out firing and firing shots."
In front of heaving crowd of 83,944 at the Melbourne Cricket Ground, winger Mark Telea grabbed a try in each half, while Shannon Frizell, Codie Taylor, Will Jordan and Rieko Ioane also crossed for the All Blacks.
Australian hopes that Eddie Jones might engineer a turnaround in his second stint with the Wallabies have proven forlorn, with the team winless from their three games in the truncated Rugby Championship.
The loss was further soured by an apparent Achilles injury to veteran Allan Alaalatoa, while fellow prop Taniela Tupou suffered a rib problem.
"Gutted," said Australia's Tate McDermott.
"84,000 people showed up tonight to support us and we didn't give them much."
The home side got off to a rough start, with Tate McDermott rammed over the try-line by Scott Barrett at a line-out and Shannon Frizell scooping up the loose ball to touch down before the third minute was up.
The Wallabies responded four minutes later, with Mark Nawaqanitawase providing the spark with a line-break, allowing Rob Valetini to burrow over under the posts four minutes later after a multi-phase attack.
But that was as good as it got for Jones's strugglers.
They were soon camped on their own try-line defending a barrage of punishing drives.
Penalised off-side, they were caught napping as Telea took a quick tap to gallop over by the posts but the winger failed to put boot to ball and the try was cancelled.
For all that, Telea's non-try heralded a dismal period for the hosts.
Winger Marika Koroibete was given a yellow card for deliberate off-side and the All Blacks were soon celebrating their second try when Codie Taylor rumbled over from a clinical line-out drive.
Rookie flyhalf Carter Gordon's restart kick failed to clear the 10-metre line and Alaalatoa was hurt in the scrum, then carted off ground.
The All Blacks capitalised on Australia's woes, with Richie Mo'unga popping a pass wide to Jordan who danced around a nest of defenders for a try at the right corner.
Mo'unga's conversion put the All Blacks up 19-7 at halftime, and they held firm after the break, twice denying the Wallabies tries with stonewall defence on the line.
With Tupou grimacing on the bench, Australia had a second yellow card when replacement prop Angus Bell was sent off for a high tackle on Nepo Laulala.
Undermanned, the Wallabies promptly collapsed, conceding three tries in seven minutes as the All Blacks ran riot.
Clarke started the burst with a try at the left corner on the hour-mark, before Telea grabbed his second on the right and Rieko Ioane completed a scintillating team try in the 67th minute.