Thomas Luthi claimed his maiden Moto2 pole position at Sepang, but the big story of the session was that Stefan Bradl qualified 34 places ahead of his title rival Marc Marquez.
Marquez, who goes into the penultimate race of the year three points behind Bradl, has been in pain since a heavy crash on an unflagged wet area right at the start of Friday practice.
The Spaniard sat out the rest of practice before returning to the track for qualifying, where he did the required two laps to qualify and took 36th on the 37-bike grid.
Meanwhile Bradl held provisional pole until the closing minutes, when Luthi slipped ahead by 0.212 seconds.
Bradl can clinch the title tomorrow if he wins and Marquez is lower than 13th.
Michele Pirro earned his first Moto2 front row start even though he crashed twice. His time held for third despite a late improvement by his Gresini team-mate Yuki Takahashi, who took fourth.
The Espargaro brothers complete row two, with Pol ahead of Aleix.
Marc VDS duo Mika Kallio and Scott Redding line up seventh and ninth, sharing row three with Claudio Corti. Mattia Pasini was the final man in the top 10.
Having broken his collarbone in a crash at the same time as Marquez, Bradley Smith will miss this weekend's race.
Pos Rider Team/Bike Time Gap
1. Thomas Luthi Interwetten Suter 2m07.512s
2. Stefan Bradl Kiefer Kalex 2m07.724s + 0.212s
3. Michele Pirro Gresini Moriwaki 2m08.004s + 0.492s
4. Yuki Takahashi Gresini Moriwaki 2m08.069s + 0.557s
5. Pol Espargaro Speed Up FTR 2m08.107s + 0.595s
6. Aleix Espargaro Pons Kalex 2m08.154s + 0.642s
7. Mika Kallio Marc VDS Suter 2m08.240s + 0.728s
8. Claudio Corti Italtrans Suter 2m08.319s + 0.807s
9. Scott Redding Marc VDS Suter 2m08.412s + 0.900s
10. Mattia Pasini Ioda FTR 2m08.414s + 0.902s
11. Alex de Angelis JIR Motobi 2m08.417s + 0.905s
12. Esteve Rabat Blusens FTR 2m08.466s + 0.954s
13. Andrea Iannone Speed Master Suter 2m08.520s + 1.008s
14. Simone Corsi Ioda FTR 2m08.549s + 1.037s
15. Max Neukirchner MZ 2m08.620s + 1.108s
16. Anthony West MZ 2m08.714s + 1.202s
17. Mike di Meglio Tech 3 2m08.855s + 1.343s
18. Jules Cluzel Forward Suter 2m08.934s + 1.422s
19. Kenan Sofuoglu Technomag-CIP Suter 2m09.015s + 1.503s
20. Dominique Aegerter Technomag-CIP Suter 2m09.087s + 1.575s
21. Joan Olive Castello FTR 2m09.278s + 1.766s
22. Raffaele de Rosa Forward Suter 2m09.307s + 1.795s
23. Xavier Simeon Tech 3 2m09.315s + 1.803s
24. Valentin Debise Speed Up FTR 2m09.382s + 1.870s
25. Axel Pons Pons Kalex 2m09.472s + 1.960s
26. Santiago Hernandez SAG FTR 2m09.625s + 2.113s
27. Jordi Torres Aspar Suter 2m09.686s + 2.174s
28. Mohamad Zamri Baba Petronas Moriwaki 2m09.822s + 2.310s
29. Randy Krummenacher Kiefer Kalex 2m09.911s + 2.399s
30. Kenny Noyes Avintia FTR 2m10.319s + 2.807s
31. Robertino Pietri Italtrans Suter 2m10.348s + 2.836s
32. Ivan Moreno Aspar Suter 2m10.875s + 3.363s
33. Yonny Hernandez Blusens FTR 2m11.022s + 3.510s
34. Hafizh Syahrin Petronas Moriwaki 2m11.388s + 3.876s
35. Mashel Al Naimi QMMF Moriwaki 2m12.180s + 4.668s
36. Marc Marquez Catalunya Suter 2m12.864s + 5.352s
37. Apiwat Wongthananon SAG FTR 2m13.201s + 5.689s