Connacht duo Tiernan O’Halloran and John Cooney both appeared off the bench with Cooney making his international debut ahead of his move to Ulster next season.
28 points was the margin in Shizuoka last week and it was 22 this morning at Ajinomoto Stadium, the venue for the opening match of the 2019 Rugby World Cup. The second Test also marked Devin Toner's 50th cap for Ireland as back rowers Josh van der Flier and Sean Reidy scored their first international tries.
A third-minute intercept try from Garry Ringrose - his fourth score of his debut Test season - put Joe Schmidt's men on course for a 28-8 half-time lead. Van der Flier, Marmion and tour captain Rhys Ruddock also touched down, while busy centre Kotaro Matsushima chipped in with Japan's try.
It was a hard slog in the third quarter, the hosts' swarming defence cutting down the space and opportunities for Ireland. A ricocheting kick bounced fortuitously for winger Akihito Yamada to notch a try on the hour mark.
However, with 20-year-old lock James Ryan impressing off the bench, Ireland hit back with a fifth and final try when some neat interplay between fellow replacements Niall Scannell and Sean Reidy saw the latter raid in just to the right of the posts.
Paddy Jackson made it 11 successful kicks out of 11 in the last two games, finishing with a 10-point haul in the Japanese capital, as Ruddock, who led the new-look squad extremely well from New Jersey to Tokyo, accepted the Lipovitan D Challenge Cup on behalf of the victors.