The tourists struck in the third minute through a try by centre Gary Ringrose who finished off an interception which the visitors won in Japan's half.
Ireland scored three more tries in the first half through Josh van der Flier, Kieran Marmion and captain Rhys Ruddock.
Japan hit back in the 23rd minute after the hosts won a line out deep in Ireland's half, setting up a rampaging run by lock Uwe Helu which centre Kotaro Matsushima completed with a sweeping try in the right corner.
Jumpei Ogura also converted a penalty in the half past to add three points for Japan.
The home side came back with more intent in the second half, which it dominated for long stretches by kicking less and keeping the ball in hand.
Wing Akihito Yamada pounced on a chip kick from Rikiya Matsuda to touch down on the right corner in the 62nd minute.
While Japan's performance was an improvement since being thrashed by Ireland 50-22 a week ago in Shizuoka, their comeback stalled after Yamada's try.
Although the visiting side, shorn of 11 players away on British and Irish Lions duty in New Zealand, began to tire under the hot and humid conditions, they never let off the gas.
A try by replacement Irish flanker Sean Reidy two minutes from the hooter killed off the Japanese fightback, much to the disappointment of the 29,354 fans gathered at the Ajinomoto Stadium.
Paddy Jackson was unerring with the boot, converting all five of the tries scored by Ireland.
(Reporting by Shinichi Saoshiro; editing by Amlan Chakraborty)
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