The sides battled end to end, sticking to quick hands and making expansive runs despite wet conditions in a game at Chichibunomiya Stadium in central Tokyo to mark the 100th anniversary of the Japan Rugby Football Union.
Fiji battered Japan with powerful tackles and outran the hosts in open play but Japan took their chances while in the Fijian 22 to stay in the game.
Tied at three converted tries apiece at the end of the first half, Fiji kept up their momentum to finish ahead by two penalty conversions, even though a dangerous tackle by number 8 Motikiai Murray on counterpart Faulua Makisi in the 34th minute took them down to 14 men for 20 minutes.
Japan found success at the maul, scoring two tries off lineout mauls in the first half, but were undone by handling errors and beaten in the air, with Fiji trusting their power, pace and footwork to edge the hosts.
A thundering tackle on Japanese inside centre Charlie Lawrence forced a turnover on the Fijian 5-metre line and winger Nacani Boginisoko ran the length of the pitch before offloading to scrum half Terio Tamani for Fiji's fourth try.
Fiji had earlier displayed their flair in an attack starting on the halfway line, with an angled run by outside centre Tuidraki Samusamuvodre that dissected the Japanese defence to bring about Fiji's second try in the 14th minute.
Japanese skipper Warner Dearns led the resistance, putting in some thumping tackles of his own and muscling over for two tries.
The Brave Blossoms fought to the final whistle but couldn't string together enough phases in attack to overturn the deficit.
Both sides are now looking to the northern series of the Nations Championship that begins next month, with Fiji facing France, Ireland and Italy, while Japan will play Wales, England and Scotland.
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