The world number 61 Indian brushed aside the second seeded shuttler 21-9 21-10 in a match that lasted 30 minutes at the Singapore Indoor Stadium.
The 20-year-old from Hyderabad, who had spoilt former world and Olympics champion Taufik Hidayat's farewell in Indonesia, will next take on the winner between RMV Gurusaidutt and Wei Feng Chong in the second round.
Praneeth had lost to Yun in straight games at the Vietnam International Challenge in 2009.
Ajay Jayaram went down fighting 19-21 21-18 17-21 against fourth seed Kenichi Tago of Japan, while top seed Pengyu Du sent Anand Pawar packing 21-16 21-13 in another men's singles match.
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Another rising shuttler Sourabh Varma was defeated 17-21 17-21 by Wing Ki Wong in another men's singles opening round match which lasted for 37 minutes.
In women's singles, Arundhati Pantawane lost to world number 26 Bulgarian Petya Nedelcheva 18-21 18-21, while PC Thulasi put up a gallant fight against world number 14 Indonesian Lindaweni Faetri before going down 23-21 16-21 16-21 in an energy-sapping 66-minute match.