Honda's Dani Pedrosa will start Sunday's Malaysian MotoGP on pole position at Sepang.
The Spaniard, who was fastest in all three free practice sessions, suffered a crash early in qualifying but managed to keep top spot.
Newly crowned world champion Casey Stoner qualified second, with team-mate Andrea Dovizioso 0.171 seconds behind in third.
British rider Cal Crutchlow was 10th-fastest for Tech 3.
Despite his performances in practice, Pedrosa could not maintain his half-second advantage through qualifying.
The session saw pole position switch between the Honda Repsol trio of Pedrosa, Stoner and Dovizioso.
The 26-year-old Pedrosa had a slight worry 12 minutes in when he crashed entering the final corner. He quickly rejoined the field - but it took him until 38 minutes from the end of qualifying to return to top spot after some jousting between Dovizioso and Marco Simoncelli's Honda.
Pedrosa, who finished second in the 2010 World Championship, said: "I was trying hard for the pole and, in one section, I was going faster. Then I had some traffic and could not improve my lap time.
"But I was still able to be on pole for the second time [in 2011] and that's good. I'm hoping to do even better in the race."
On the crash, he added: "At the beginning of the session I had a small crash on the front. Then I had to get back on the bike and I was still able to go well."
World champion Stoner said: "With this humidity and heat over the weekend it's going to be a tough race."
The second row will consist of Colin Edwards, Simoncelli and Nicky Hayden.
Seven-time world champion Valentino Rossi crashed out late in the session and he will start ninth on the grid.
Sepang qualifying times:
1) Dani Pedrosa (Spa) Honda 2 minutes, 01.462 seconds.
2) Casey Stoner (Aus) Honda 2:01.491.
3) Andrea Dovizioso (Ita) Honda 2:01.666.
4) Colin Edwards (US) Yamaha 2:02.010.
5) Marco Simoncelli (Ita) Honda 2:02.105.
6) Nicky Hayden (Aus) Ducati 2:02.172.
7) Hiroshi Aoyama (Jpn) Honda 2:02.254.
8) Alvaro Bautista (Spa) Suzuki 2:02.332.
9) Valentino Rossi (Ita) Ducati 2:02.395.
10) Cal Crutchlow (GB) Yamaha 2:02.756.
1) Thomas Luthi (Swi) Suter 2:07.512.
2) Stefan Bradl (Ger) Kalex 2:07.724.
3) Michele Pirro (Ita) Moriwaki 2:08.004.
9) Scott Redding (GB) Suter 2:08.412.
1) Nicolas Terol (Spa) Aprilia 2 minutes, 13.579 seconds.
2) Hector Faubel (Spa) Aprilia 2:13.594.
3) Sandro Cortese (Ger) Aprilia 2:13.954