Ireland, a 50-22 winner a week ago, took control with four tries in the first half at Ajinomoto Stadium, venue for the opening match of the 2019 tournament.
Garry Ringrose scored Ireland's first try just five minutes in when he picked up an errant Japan pass and ran over from halfway.
Josh van der Flier, Kieran Marmion and captain Rhys Ruddock added tries with Paddy Jackson kicking the extras as Ireland took a 28-8 lead at halftime.
Japan defended better after the break and was rewarded when Akihito Yamada crossed to cut the lead to 28-13.
Sean Reidy scored a late try converted by Jackson.