Ireland, a 50-22 victor a week ago, took control with four tries in the first half at Ajinomoto Stadium, venue for the opening match of the 2019 tournament.
"Obviously the players are disappointed to lose the test match but I think we showed our ability against a very strong team", said Japan head coach Jamie Joseph.
Japan's line-speed and aggression in defence was noticeably improved from last weekend's abject display at Ecopa Stadium, but Ireland's power game and quick recycling was again proving too much.
Ireland was missing 11 players involved in the British and Irish Lions tour to New Zealand, and used the tests against Japan to give younger players worldwide experience.
Gust of wind gets the better of weatherman Deric Hartigan this morning
Speaking to camera calmly and smoothly, the wind attacks suddenly and unexpected and soon Deric is no longer to be seen. For those interested, the weather in Dublin on Friday was warm and partly cloudy with winds gusting up to 30 km/h.
"I think, having just spoken to the players, that was very, very tough going", said Schmidt.
Ireland overpowered Japan 35-13 on Saturday for their second straight win over their hosts to finish with a flawless record in their three-game summer tour. "It's certainly our biggest test of the tour and we had to work very hard to get the win".
"It was very hot out there and the players were fatiguing early in the game, so it was great to get a good start", Ireland coach Joe Schmidt said.
The signs were ominous for Japan's "Brave Blossoms" when Garry Ringrose raced clear to score under the posts and flanker Josh van der Flier wriggled over in the corner in the first 10 minutes.
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Japan got their second try on 61 minutes. "It's unfortunate but we didn't go into our shells after that".
That proved to be temporary respite, however, as Ireland charged back with their fourth try in the 31st minute. Matsushima turned defense into attack with a well-placed kick into Irish territory, and the same player was there to finish off the move after Uwe Helu had punched a hole in the opposition back line.
From a scrum in the Japanese 22 Jack Conan broke off the back and was stopped close to the line, the ball was quickly recycled and Ruddock barged over, Jackson's conversion gave Ireland a 28-8 lead at the interval. A ricocheting kick bounced fortuitously for winger Akihito Yamada to notch a try on the hour mark. "If we had been able to take one of them, it could have been a better game for us".
Had Nagare's try stood, Yamada's effort could have set up a tense finish but instead the hosts were left with too much to do and Sean Reidy added late gloss to the scoreline for Ireland, Paddy Jackson ideal with the boot as he knocked over his fifth conversion. Today, they gave away a lot of penalties around the ruck.
Londoners in temporary housing after fire safety evacuations
The fatal fire was started by a faulty Hotpoint fridge-freezer in one of the apartments, London police said on Friday. She told Sky News that a rest centre had been set up and residents were being found hotels and other accommodation.
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