The Brave Blossoms did not have it all their own way against a tough Chilean side, but got the job done thanks to tries from Folau Fakatava (2), Jone Naikabula, Michael Leitch, Ryoto Nakamura and Warner Dearns.
Chile, playing on the world stage for the first time, left with their pride intact, scoring two tries through Rodrigo Fernandez and Alfonso Escobar to introduce themselves in style.
A huge shock seemed possible after an electric start by the South Americans was rewarded with a seventh-minute try as Fernandez stole a loose ball after a good run by Ramon Ayarza.
Dreams were quickly shattered, though, as Japan hit back immediately with Fakatava powering through attempted tackles.
They went ahead on the half-hour as Naikabula burst over the line from a scrum before Fakatava got his second try on the stroke of half-time.
Escobar brought Chile back into it early in the second half as he carried over the line after a prolonged attack, reducing the deficit to 21-12.
Japan - who reached the quarter-finals at their home World Cup four years ago - closed out the win though, with Leitch running clear in the 53rd minute, Nakamura side-stepping a defender soon after and Dearns completing the victory a minute from the end.
Additional reporting by Press Association.