In the first half fullback Ange Capuozzo, scrum-half Martin Page-Relo and lock Andrea Zambonin crossed the line, with all three tries converted by flyhalf Paolo Garbisi.
Page-Relo also hit a long-range penalty put the Azzurri 24-0 up.
Japan centre Dylan Riley took advantage of some poor defending to score two tries either side of half time and help bring the hosts back to 24-14.
But the visitors cruised home with two more penalties by Page-Relo and tries by substitute and Garbisi’s scrumhalf brother Alessandro and flanker Ross Vintcent.
The only bad news for Italy was that Paolo Garbisi had to be stretchered off in the second half after taking a nasty blow to the head.
Italy lost the first game of the tour to Samoa and beaten Tonga in the second match.
ANSA
