Fabio Quartararo stormed to pole as Yamaha locked out the front row while Marc Marquez will start the Malaysian MotoGP in 11th after crashing on Saturday.
Quartararo said Petronas Yamaha SR would need to go even quicker in qualifying for their home race after twice smashing the lap record during practice in Sepang on Friday.
The Frenchman duly took first place on the grid ahead of Maverick Vinales (Monster Energy Yamaha MotoGP), with Quartararo's team-mate Franco Morbidelli taking third place.
Quartararo clocked a sensational one minute 58.303 seconds on his last qualifying lap to take pole.
Marquez suffered a massive highside at Turn 2 in the second qualifying session when hunting 20-year-old rookie Quartararo for a tow.
The world champion was able to pick himself up after that dramatic smash, but will have to come from a long way back on Sunday.
Jack Miller heads up the second row ahead of Cal Crutchlow, quickest in Q1, and Valentino Rossi.
Andrea Dovizioso could only qualify in 10th spot as Quartararo celebrated his fifth pole of the season.
1. Fabio Quartararo (Petronas Yamaha SR): 1:58.303
2. Maverick Vinales (Monster Energy Yamaha) +0.103s
3. Franco Morbidelli (Petronas Yamaha): +0.129s
4. Jack Miller (Pramac Racing): +0.422s
5. Cal Crutchlow (LCR Honda): +0.648s
6. Valentino Rossi (Monster Energy Yamaha): +0.697s
7. Alex Rins (Suzuki Ecstar): +0.787s
8. Danilo Petrucci (Ducati): +0.794s
9. Johann Zarco (LCR Honda): +0.836s
10. Andrea Dovizioso (Ducati): +0.870s
11. Marc Marquez (Repsol Honda): +0.875s
12. Franesco Bagnaia (Pramac Racing): +1.337s