Chou saw off fourth seed Tommy Sugiarto to book his place in the final but his momentum was checked as Wang stormed through the first game by a 21-10 margin.
But the rising star showed a strong temperament to stand alongside his burgeoning talent as he edged a tense second game 25-23 to level the contest.
It was a similar story in the deciding game before Chou prevailed 21-19 to conclude an engrossing one hour and 14 minutes on court.
Unfortunately, the ladies final could not produce a similar spectacle, with China's Olympic champion Li Xuerui taking the title as her compatriot Wang Shixian withdrew due to injury.
World number one Li was 21-15 8-3 ahead of the second seed when the premature conclusion arrived.
The manner of the win does little to take the gloss off a remarkable year for Li, who has reached the final all 10 tournaments entered during 2014.