Thomas Luthi claimed his first 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 0.212sec. 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.