The junior All Blacks had won the first four versions of the age group rugby title but were shut out by the Australians in the final match of the tournament at Bond University on the Gold Coast.
Flyhalf Will Harrison contributed 14 points from the kicking tee and Triston Reilly and captain Fraser McReight both crossed for tries but the victory was built on uncompromising defence.
McReight said the victory would give the junior Wallabies a huge boost going into the world under-20 championship in Argentina in June.
"I don't think an under-20s side has ever done that (to New Zealand) in a very long time," he said.
"We can take confidence in that, and that's so unreal and I can't wait for the future, and I can't wait to win that Junior Rugby World Cup."
New Zealand have won six of the 11 world under-20 championships since the tournament started in 2008, while Australia's best finish was a poor second behind the junior All Blacks in 2010.
In the senior ranks, Australia last held the Bledisloe Cup in 2002, with New Zealand having kept an iron grip on the symbol of trans-Tasman Sea rugby supremacy for the last 16 seasons.
(Reporting by Nick Mulvenney, Editing by Peter Rutherford)
