Chen, who triumphed at the World Championships in August, was heavily favoured to once again win a trophy he last lifted in 2012.
But he was edged out in Sunday's final of the Superseries event, as sixth seed Son produced an upset.
In a closely fought opener, Son held his nerve on a third game point to take it 21-19.
The South Korean then used that momentum to take the second, winning it 21-16 to seal his triumph.
There was no such upset in the women's final as Nozomi Okuhara's fairytale run came to an end.
Okuhara would have been brimming with confidence after she stunned world and European champion Carolina Marin to book her place in the final.
However, she came up short against world number six Tai Tzu-ying, who won 21-19, 21-11 inside 50 minutes.
Chinese Taipei's Tai produced a fast start to claim an 11-5 lead in the opener, only for her opponent to reel off five successive points.
Tai assumed full control thereafter, though, finishing the job with a comprehensive showing in the second game.