Japan recovered from going 14-0 down to lead 17-14 at half-time before the European side eventually prevailed by four tries to three.
Matteo Pratichetti, Edoardo Gori, Leonardo Ghiraldini and Andrea Lo Cicero touched down for the hosts, Riccardo Bocchino kicking three conversions, with Japan's scores coming from Takeysa Usuzuki, Koji Taira and a penalty try.
The Azzurri looked on their way to an easy win when Pratichetti and Gori crossed the whitewash in the opening 12 minutes, but the visitors hit back through tries from Usuzuki and Taira and some faultless kicking from James Arlidge.
The Italy pack proved too hot for Japan to handle in the second half, though, as Ghiraldini put the hosts back in front following a rolling maul.
Lo Cicero added a fourth try, converted by substitute Luciano Orquera, before he was yellow-carded moments later and Japan were awarded a penalty try as Italy came in at the side of their driving maul.
Japan's hopes of another fightback were dealt a blow when prop Hisateru Hirashima was sin-binned and Italy held firm, with Orquera kicking a penalty to increase their lead.
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