After the Kangaroos took a 12-8 lead into halftime, the home side hit the front when hooker Brandon Smith burrowed over in the 54th minute.
The try gave New Zealand a 26-12 lead and it needed every point as Australia scored late tries through Felise Kaufusi and James Tedesco to slash the lead to two points with two minutes remaining.
Auckland's Mt Smart Stadium played host to a triple-header between the fierce sporting rivals on Saturday.
The Kangaroos' new era began with a 26-24 defeat to the Kiwis at Mt Smart Stadium, an outcome which indicated there are set to be some growing pains after farewelling some of Australia's all-time greats.
It was the first time in six years that New Zealand have beaten their nearest neighbours and reigning World champions. "They took it up for the crowd and our country and did our families proud".
"We came into camp to build foundations not only for us going forward but the Kiwis coming through and the kids after that", Watene-Zelezniak.
The North Queensland playmaker had a hand in most of the Australian under-20s' best moments to earn man-of-the-match honours in the seven-tries-to-five victory on Saturday.
After Valentine Holmes had touched down and added the extras to his own try inside three minutes, Ken Maumalo and Joseph Manu crossed for the Kiwis, but Shaun Johnson missed both conversions.
With Greg Inglis suspended and Cameron Smith, Johnathan Thurston, Cooper Cronk and Billy Slater having retired, the Kangaroos looked far from the dominant force which has reigned over the rugby league world for so long.
The loss of Keary in the 17th minute was a blow for Australia but Meninga was able to call St George Illawarra halfback Ben Hunt off the bench.
New Zealand trailed 12-8 at the break despite dominating possession and territory in the opening period.
"If we can do it for each other then the fans will just come on board and ride the wave with us", Watene-Zelezniak said.
"People like Kevin Proctor and Jesse Bromwich, they've faced adversity and what we saw, to come back in form the way they did", Maguire said.
A rare loss against New Zealand in Auckland may give giant-killing Tonga hope for the one off Test match against Australia next week and coach Mal Meninga admits the Kangaroos have "a bit of work to do".