Charles Piutau (two), Sam Cane, Ben Smith, Richie McCaw, Jeremy Thrush, Frank Halai, Beauden Barrett all scored tries for the All Blacks, who efficiently put away their scoring opportunities but were let down by messy patches.
Fly-half Daniel Carter added five conversions while Barrett added two late conversions.
Japan full-back Ayumu Goromaru slotted two first half penalties for the home side, who were hemmed inside their own territory for much of the game but will take heart from their improved performance.
The match was significant for being the first outside of a World Cup between the two sides, with the All Blacks having recorded victories of 145-17 and 83-7 and few had expected the result on Saturday to be any different.
The world champions had said they wanted to use the match to introduce some of their less experienced players to Test rugby, with nine players sent directly to Paris to prepare for their clash with France next week.
New Zealand coach Steve Hansen gave starts to Dominic Bird and Halai and also introduced Jeffrey Toomaga-Allen and Luke Whitelock off the bench to bring the total of new caps to 21 since he took over following the 2011 World Cup.
"It was a very good game for us in a number of ways. We got some new people on track, they got some experience and understood what its like to be an All Black," Hansen told reporters.
"We got Richie (McCaw) and Dan (Carter) back on track and they got some time."
Japan had a troubled build-up with coach Eddie Jones hospitalised with a stroke last month and assistant Scott Wisemantel taking over the reins for their November Tests.
The 'Brave Blossoms' had been buoyed by their first win over an inexperienced and depleted Wales side in June and Wisemantel said the rare meeting with the All Blacks was a chance to show the world they were improving.
That was only too evident in the gloomy and wet conditions where the Japanese were combative at the scrum, despite a significant weight disadvantage, and clinical at the lineout where they also conTested on New Zealand's throw.
"The Japanese put us under pressure at times. Their scrum was pretty good, they scrummaged well," said New Zealand captain McCaw.
All Black prop Ben Franks concurred, saying Japan's low scrum, which pushed back the visiting pack on a few occasions, gave them trouble.
The visitors superior ball handling at pace, however, proved the decisive factor with the All Blacks striking from deep, running into space and exploiting the home side's mistakes inside their own half to record the comfortable victory.
Japan still drew solace from the fact that they kept the point differential below the half century mark for the first time against the toughest of opponents.
"We did really well in the first 20 minutes. The next step is we need to maintain it against those types of teams for 50 minutes to keep the pressure," Japan's stand-in coach Wisemantel said.
"We gave away a few cheap tries and that's where we let the game slip."
The home crowd, who painted the sold out stadium red, greeted Japan's rare attacking chances with enthusiasm, with excitement reaching a crescendo in the last minute of the match when Japan wing Kenki Fukuoka almost scored a try in the corner.
"We were disappointed we could not get a try since there were attacking opportunities to take advantage of. But we come away from the game confident we are on the right track," Japan captain Toshiaki Hirose.
The All Blacks, who have now won all 11 of their Tests this year, head to Paris to meet France on November 9, while Japan will play Scotland at Murrayfield in Edinburgh.
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