Wong Chin Hung fired his spot kick past goalkeeper Takuya Matsumoto to give Hong Kong a 4-2 victory in the shootout after 90 minutes of regulation and 30 minutes of extra time finished 1-1.
Hong Kong become the first winners of the title from outside East Asia's top three footballing nations, Japan, South Korea and China.
Nearly 32,000 fans packed into the Hong Kong Stadium for the final, which brought a close to the eighth of the nine days of action at the quadrennial Games.
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