Sonny Bill Williams and Sam Cane also crossed over before Nonu's special moment three minutes from time as the World Cup favourites eventually won by a convincing 47-9 margin.
Tonga could only register three Kurt Morath penalties, leaving the New Zealanders to top Pool C with a near-perfect tally of 19 points.
Steve Hansen's team had already booked a place in the quarter-finals - where they are set to face Ireland or France - after three straight wins over Argentina, Namibia and Georgia but their displays had been far from slick.
And for spells they were just as disjointed against the Pacific Islanders, but o nce they did get motoring they simply blew Tonga away.
The world champions ran out without inspirational captain Richie McCaw, who was wrapped in cotton wool - and left to carry the water bottles - after sustaining a slight hip strain.
But it was still largely a first-choice XV put out by Hansen, with centre Nonu joining an elite band of just six men who have reached a century of appearances for the All Blacks.
While New Zealand's place in the last eight was already guaranteed, the Tongans knew only an unlikely victory would salvage their chances of claiming third place in the group and automatic qualification to the 2019 World Cup in Japan.
However, despite battling with a determination and ferocity, they could not upset the odds as New Zealand powered on to a routine victory.
It was a Tongan mistake which allowed the All Blacks to go in front after 14 minutes. Hooker Elvis Taione overcooked a line-out and a swift counter attack saw New Zealand romp up-field before Ben Smith was the benefactor of some neat interchanges down the narrow side to run in for the opener, converted by Dan Carter.
Morath put the Tongans on the scoresheet with a penalty but New Zealand scored again when they moved the ball with pace off the back of a scrum, allowing prop Woodcock ample time to bundle over after 31 minutes. Again Carter put over the extras.
Ben Smith was spared a stint in the sin-bin when he dumped Telusa Veainu on his back but Kieran Read was not so lucky as the Tongans put the pressure on just before the break.
Whatever Hansen said at half-time, it worked as his team returned with a more focused eye.
Although Morath trimmed the deficit slightly with another penalty, New Zealand quickly added to their tally as they forced the Tongans back, patiently working through the phases before Carter spread the ball wide for wing Milner-Skudder to dive over for another converted touchdown.
Another Morath penalty was reward for his side's tenacity but their losses continued as Milner-Skudder raced on to Ben Smith's grubber to put the scoring touch on a fourth try, converted by Carter.
With Tongan resistance wilting, substitute Williams was allowed to drive through the heart of their defence to add another score, leaving Carter with another simple kick for the extras.
Things went from bad to worse for Mana Otai's team when prop Paula Ngauamo was handed a yellow card for another dangerous drop tackle on Carter. With their defensive shape undone, Cane cantered in for his 10th international score while Carter was again flawless with the conversion.
But the biggest cheer of the night was reserved for Nonu as he raced down the left wing to put a gloss on his milestone occasion with the seventh try. Carter's boot finally failed him though as he tugged the conversion.
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