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
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.
A 14-member India squad will be chosen at the tryouts to compete in the forthcoming Badminton Asia Mixed Team Championships, which will take place in Dubai from February 14 to February 19.
The Satwik-Chirag team, which last week won the French Open, overcame a deficit in the first set to defeat the Chinese Taipei team 19-21, 21-19, and 21-16 in 61 minutes.
The fourth-seeded Indian saved six match points in the second game, but lost the final 21-14, 22-20 to become only the fourth Indian to win a silver medal in the competition.