This was Sen's second straight defeat at the hands of Chou in less than a month.
It was the world No 6 Zii Jia's second title on the trot after winning the Asian crown in Manila earlier this month.
Women's doubles pair of Treesa Jolly and Gayatri Gopichand also jumped 12 places to reach a career-best world No. 34.
The youngster won his first BWF Super 100 title in Cuttack on Sunday.
Srikanth went down to Loh Kean Yew of Singapore in the summit clash.
Defending champion Sindhu faces top seed and world No. 1 Tai Tzu Ying of Chinese Taipei in the quarterfinals.
Prannoy came back to win 13-21, 21-18, 21-19 in a contest that stretched to one hour and 11 minutes.
The reigning world champion had no answer to the in-form world No. 6, who dictated terms from the word go.
Indian youngster Lakshya Sen lost to Denmark's Viktor Axelsen 13-21, 11-21 in the men's single semifinals.
Kidambi Srikanth bowed out of the tournament after losing to second-seeded Malaysian Lee Zii Jia 19-21, 14-21.