The unseeded Prannoy outplayed top seed Wei 21-10, 21-18 in a match which lasted around 40 minutes, reports Xinhua news agency.
The 34-year-old seasoned Malaysian player won Indonesia Open super series in 2007, 2009, 2010, 2011, 2013 and 2016. His champion record in the annual tournament is comparable to Indonesian players Taufik Hidayat and Ardy B. Wiranata.
"I, of course, cannot win all tournaments. But I would try my best to get my seventh championship title in Indonesia Open," the six-time champion of the tournament said on the sidelines of his match held in Jakarta Convention Center (JCC) here.
After winning the crucial match, Prannoy said that the Malaysian player was not in his best condition made him win the qualifying match
"I did not have prediction to win this match. All I did was trying to play more aggressive," Prannoy said.
In the upcoming quarterfinal match, the Indian shuttler would take on the winner of a qualifying match between China's seeded player Cheng Long and Indonesian player Jonatan Christie.
In the previous men's singles match on Wednesday, China's Olympic and World champion Lin Dan was surprisingly defeated by Chinese Taipei non-seeded contender Wang Tzu Wei in two straight sets.