Championship leader Marc Marquez set a new lap record on his Honda to take pole for Sunday's Malaysian MotoGP.
Marquez, who leads by 39 points with four races left, clocked two minutes 00.011 seconds on his final lap to beat Valentino Rossi and Cal Crutchlow.
Yamaha's Jorge Lorenzo, second behind his fellow Spaniard in the standings, will start from fourth place in Sepang.
Honda's Stefan Bradl, sixth in the championship, will miss the race after fracturing his ankle in practice.
The German lost control of his satellite LCR Honda and appeared to catch his ankle in the artificial grass around the corner of the track.
The 23-year-old will now fly to Barcelona for surgery on Monday.
Bradl, who had been challenging Crutchlow for fifth and top satellite honours in the championship, is now a major doubt for Australia next weekend and Japan - the penultimate round of the season - in a fortnight's time.
Briton Crutchlow, fifth overall, led into the final minute after recording 2:00.359 on his Tech 3 Yamaha but seven-time world champion Rossi posted 2:00.336 for Yamaha before Marquez went even quicker.
It is the 20-year-old's eighth pole of 2013 and his fourth in succession.
Crutchlow told BBC Sport: "It's going to be very difficult. I've got a bad pain in my right arm from Silverstone that needs an operation but we pushed hard for that.
"I'm pleased for the whole team. We've worked endlessly all weekend and hopefully tomorrow will be a good race for us."
Malaysian MotoGP qualifying result:
1. Marc Marquez (Spain) Repsol Honda 2:00.011
2. Valentino Rossi (Italy) Yamaha 2:00.336
3. Cal Crutchlow (Britain) Tech 3 Yamaha 2:00.359
4. Jorge Lorenzo (Spain) Yamaha 2:00.578
5. Dani Pedrosa (Spain) Repsol Honda 2:00.692
6. Alvaro Bautista (Spain) Honda Gresini 2:00.974
7. Bradley Smith (Britain) Tech 3 Yamaha 2:01.306
8. Andrea Dovizioso (Italy) Ducati 2:01.635
9. Aleix Espargaro (Spain) ART 2:02.151
10. Andrea Iannone (Italy) Ducati 2:02.536