The two Indian men's doubles pair of Dhruv Kapila and M R Arjun and Satwiksairaj Rankireddy and Chirag Shetty also moved into the quarterfinals.
Sen defeated Spain's Luis Penalver 21-17 21-10 in the BWF World Championships in Tokyo on Wednesday.
Ashwini Ponnappa and N Sikki Reddy progressed to the women's doubles second round.
Sindhu outplayed Michelle Li of Canada 21-15, 21-13, while Sen rallied to down Malaysia's Ng Tze Yong 19-21, 21-9, 21-16 in a thrilling men's singles final.
Badminton offers India a chance to land three more gold medals.
Sindhu rode on her technical superiority to outwit Singapore's Yeo Jia Min 21-19, 21-17 in a 49-minute contest.
The men's doubles pair of Satwiksairaj Rankireddy and Chirag Shetty also entered semifinals.
This was Prannoy's first-ever win against Sen out of their three head-to-head meetings so far.
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.