Sen defeated Prannoy 21-14, 21-15 in the men's singles to settle his score against the World No 9 after he had suffered a defeat in the Malaysia Open earlier this month.
The Indian duo, who had lost the first set, was trailing 17-10 in the second and appeared poised to defeat but the ace shuttlers ranked fifth in the world in men's doubles, made a stunning comeback to win the match 17-21, 22-20, 21-9.
The Japanese shuttler had a 2-0 head-to-head advantage over Prannoy going into their quarterfinal matchup on Friday at the opening BWF World Tour event of the season
In their round of 16 match, the duo defeated the Indonesian duo of Muhammad Shohibul Fikri and Bagas Maulana in their round of 16 match in straight two games
Since Marin defeated Sindhu in the Swiss Open final in 2021, this was the first encounter between the Rio 2016 finalists. It was PV Sindhu's first game following her gold medal victory at the 2022 Commonwealth Games in August.
World Championships bronze medallists Satwiksairaj Rankireddy and Chirag Shetty got the better of the Korean duo of Choi Sol-gyu and Kim Won-ho by 21-16, 21-13 in the first round of the tournament.