Japan led 17-14 at the break, but second-half tries from Leonardo Ghiraldini and Andrea Lo Cicero helped Italy finally tame the battling visitors.
Italy grabbed an early opener when Riccardo Bocchino sent Matteo Pratichetti under the posts and Edoardo Gori soon added a second when he dived over the line.
But Japan produced a superb response as Takeysa Usuzuki raced onto a kick before Koji Taira burrowed over and James Arlidge's penalty gave them a half-time lead.
Italy turned to their pack in the second half and a driving maul resulted in a try for Ghiraldini, while Lo Cicero drove through a pile of bodies to score.
Japan did reduce the deficit with a penalty try after Italy were punished for coming in from the side, but Luciano Orquera's penalty rounded off the night's scoring.
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