By virtue of the win, world No. 9 Bing Jiao, whom Sindhu had defeated at the Badminton Asia Championship, leads the Indian 10-8 on head-to-head record.
This was Sen's second straight defeat at the hands of Chou in less than a month.
Sen defeated Rasmus Gemke 21-18 21-15 while Sindhu edged Gregoria Mariska Tunjung 23-21 20-22 21-11.
Sen, who was part of the Indian team that claimed a historic Thomas Cup triumph in Bangkok, prevailed 21-18, 21-15 over world No. 13 Gemke in 54 minutes.
World championship bronze medallist Sen outwitted Denmark's Hans-Kristian Solberg Vittinghus 21-10 21-18.
Sindhu, a two-time Olympic medallist, lost 17-21, 16-21 to third seeded Chen in 43 minutes to end an impressive run in the Super 500 tournament.
The sixth seeded Indian prevailed 21-15 20-22 21-13 over the Japanese in 51 minutes.
The world no took just 37 minutes to get the better of Sim Yu Jin, 21-16 21-13.
World No. 7 Sindhu was off colour for the second consecutive day as she squandered a game lead to go down 21-18, 17-21, 12-21 to Intanon, ranked eighth, in a 59-minute first women's singles match.
The Indian women humbled USA 4-1 to notch up their second successive win in Group D.