The unseeded Prannoy outplayed top seed Wei 21-10, 21-18 in a match lasting 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.
After winning the crucial match, Prannoy said that the Malaysian player was not at his best.
"I did not have prediction to win this match. All I did was trying to play more aggressive," Prannoy said.
In the upcoming quarter-final 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 other men's singles match, Kidambi Srikanth defeated fourth seed Jan O Jorgensen of Denmark to advance. The Guntur-born player took around one hour to beat his opponent 21-15, 20-22, 21-16.
In women's singles category, it was a bad day for Saina Nehwal and Rio Olympic Bronze medallist P.V. Sindhu as they lost their matches and bowed out of the tournament.
Saina was beaten by Thailand's Nitchaon Jindapol 15-21, 21-6, 16-21 in a marathon match of over one hour while fourth seed Sindhu was outplayed by Beiwen Zhand of the US 21-15, 12-21, 18-21.