It was the first time in six years that New Zealand have beaten their nearest neighbours and reigning World champions.
Manu was then controversially ruled to have knocked on before his chip led to Dallin Watene-Zelezniak scoring and the Kangaroos hit back with a sucker-punch, Tom Trbojevic breaking clear to put Dane Gagai over for a try Holmes converted.
It was the Kiwis' first win over the Kangaroos since the 2015 Anzac Test.
Heading into tonight's Test against Australia at Mt Smart Stadium, the Kiwis have a fight on their hands for the hearts and minds of the New Zealand rugby league public. The Tongan people are prideful about their country and where they come from.
"We are still building, We have only set the foundations now but we have to keep building".
Kiwis coach Michael Maguire discusses what was said at halftime to spur his side to victory over Australia at Mt Smart.
But the Kiwis fielded a strong side, including several players who featured in the Sydney Roosters win over Melbourne in last month's National Rugby League grand final.
While New Zealand dominated possession and territory in the first half, Australia began and ended the spell with tries which gave it a lead at halftime. Ultimately, they weren't good enough to take advantage of the field position and it was Kiwi rookie Brandon Smith who got over the line first in the second half when he chose to take a dart from dummy half on last tackle.
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Valentine Holmes and Lattrell Mitchell were a unsafe attacking combination down the left-hand side and they created Australia's first try, to Holmes, after only two minutes. They were on the wrong side of a 36-18 match.
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.
"It feels so surreal", Watene-Zelezniak said.
Australia's late rally put the Kiwis under pressure but the were able to see off the threat.
"It was always going to be a bit clunky at times", Cook said.
"We didn't give ourselves much chance but we stuck in there and it was a tight finish", he said. "Our ball control was pretty disappointing".
The Kiwis are next in action when they travel to the United Kingdom for a three-Test series against England later this month.