Spain's Sergio Garcia, who was tied for the lead after the second round, struggled with his game and finished in a tie for 19th place after a 77 on the final day left the Spaniard at 4-under 284.
Garcia had two double bogeys, three bogeys and a pair of birdies in his final round at the Gotemba Course.
Nakajima carded three birdies on the front nine before widening his lead with four more birdies after the turn to finish at 13-under 275. Taniguchi finished at 12-under 276 after a 67.
Two-time defending champion Darren Clarke tied for 44th after a final round 75.
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