The Commonwealth champions took the first game 21-13 against Baek Ha-na-Lee Yu-lim of South Korea, but then went down 19-21 in the second game.
After trailing 11-16 in the rubber, a tearful Pearly decided to call it a day and had to leave the court in a wheelchair.
The South Koreans go through to the last eight of the tournament.
Only three Malaysian representatives survived the second round of the Japan Open.
Professional men’s doubles pair Ong Yew Sin-Teo Ee Yi stormed into the quarterfinals after they took 33 minutes to beat French duo Christo Popov-Toma Junior Popov 21-13, 21-13.
Yew Sin-Ee Yi will go up against Choi Sol-gyu-Kim Won-ho in the last eight after the South Korean duo beat Indonesia’s Leo Rolly Carnando-Daniel Marthin 21-15, 21-13.
Independent mixed doubles pairs – Tan Kian Meng-Lai Pei Jing and Hoo Pang Ron-Toh Ee Wei – also made the quarterfinals.
Kian Meng-Pei Jing, seeded seventh, prevailed against Taiwanese pair Yang Po-Hsuan-Hu Ling Fang 14-21, 21-11, 21-15.
World Championships bronze medallists Wang Yi Lyu-Huang Dong Ping await Kian Meng-Pei Jing in the next round after the Chinese pair trounced Rinov Rivaldy-Pitha Haningtyas Mentari of Indonesia 21-13, 21-18.
A mammoth task lies ahead for Pang Ron-Ee Wei as they will have to slog for a semifinal spot against current world champions Zheng Si Wei-Huang Ya Qiong of China tomorrow.
Pang Ron-Ee Wei subdued Dutch duo Robin Tabeling-Selena Piek 29-30, 21-18, 21-11 while Si Wei-Ya Qiong eliminated Supak Jomkoh-Supissara Paewsampran from Thailand 21-7, 21-11.
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