Despite beating China 7-0 at home in September, it took Japan 39 minutes to break the deadlock in Xiamen with a Koki Ogawa header. Ko Itakura added a second before halftime.
Home fans grew hopeful when Lin Liangming scored early in the second half but Ogawa headed home his second soon after.
The Samurai Blue have 16 points from six games, with four to go in Group C. Australia is next with seven points after Kusini Yengi scored in the 96th minute to earn a dramatic draw for the Socceroos in Bahrain.
The Portsmouth forward opened the scoring in the first minute but two second-half goals from Mahdi Abduljabbar put the hosts in sight of a famous victory before Yengiās late intervention. Bahrain is one of four teams on six points along with Saudi Arabia, Indonesia and China.
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