Lin was left puzzled by his rival's performance
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Lin Dan won the Japan Open after an Indonesia's volatile Taufik Hidayat suffered a meltdown in Sunday's final.
Lin triumphed 16-21 21-16 21-3 to continue his rich vein of form after the Chinese world number one captured the world title in Madrid last month.
But Taufik's collapse in the final game took some of the gloss off his win.
Lin said: "I couldn't cope with his speed in the first game, but Taufik seemed to give up when I took the lead in the third."
Former world number one Taufik was docked ranking points after storming out of a match against Lin at the Hong Kong Open in August in protest at a line call.
Women's number one Zhang Ning saved three match points to beat fellow Chinese Xie Xingfang 21-11 16-21 30-29 in their earlier singles final in Tokyo.