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The match continued to be close until the 30th minute, when Julian Savea ran in the first of three quick tries for the All Blacks, opening up a 34-10 lead.
Geoff Cross reduced the deficit for the home team with a try on the stroke of half-time.
Scotland were handed a lifeline early in the second half when New Zealand were reduced to 14 men.
Scotland used their one-man advantage to get Visser's second try of the game.
A fifth New Zealand try gave the world's top ranked side a big enough lead, as they eased off on the attack in the final 15 minutes of the game, only Ben Smith troubling the Scotland defence to add a sixth.
Scotland face South Africa in their next match, while New Zealand travel to Italy.