Dani Pedrosa took his first pole position of the season as MotoGP returned from the summer break at Brno.
The Spaniard pipped compatriot Jorge Lorenzo and Repsol Honda team-mate Casey Stoner in a tight qualifying session in the Czech Republic.
Ben Spies was fourth on his Yamaha with Marco Simoncelli fifth and Valentino Rossi sixth.
British rider Cal Crutchlow was down in 11th after walking away unscathed from a late crash.
Pedrosa told BBC Sport: "It's my first pole in a long time.
"The weekend is going well and I hope the bike will improve for tomorrow. The track conditions were not easy but I am confident for a good race."
Lorenzo added: "We changed the bike and it has improved a lot. I am very happy with second and I am out to take some points from Casey tomorrow."
Simoncelli set the early pace and Crutchlow was briefly up in third spot before the Hondas of Pedrosa and Stoner took to the top of the timesheets.
Lorenzo split the team-mates before moving into top spot with quarter of an hour remaining.
Crutchlow then crashed his Tech 3 Yamaha and Pedrosa moved into provisional pole position with a flying lap.
Lorenzo mounted a late charge but could not quite take top spot.
Earlier, Stoner crashed out of wet practice on Saturday morning but still managed to clock the fastest time ahead of Lorenzo and Rossi - but there was bad news for wildcard John Hopkins.
The British Superbike rider also crashed out in practice but broke three fingers on his right hand and was ruled out of tomorrow's race.
Czech Republic MotoGP qualifying times:
1. Dani Pedrosa (Spa) Repsol Honda 1min 56.591 secs
2. Jorge Lorenzo (Spa) Yamaha 1:56.704
3. Casey Stoner (Aus) Repsol Honda 1:56.860
4. Ben Spies (US) Yamaha 1:57.178
5. Marco Simoncelli (Ita) Gresini Honda 1:57.351
6. Valentino Rossi (Ita) Ducati 1:57.367
7. Andrea Dovizioso (Ita) Repsol Honda 1:57.442
8. Colin Edwards (US) Tech 3 Yamaha 1:57.676
9. Nicky Hayden (US) Ducati 1:57.721
10. Hiroshi Aoyama (Jpn) Gresini Honda 1:57.784
11. Cal Crutchlow (GB) Yamaha 1:57.797
1. Marc Marquez (Spa) Suter 2:02.493
2. Stefan Bradl (Ger) Kalex 2:02.704
3. Alex De Angelis (SM) Motobi 2:02.725
1. Nicolas Terol (Spa) Aprilia 2:08.118
2. Johann Zarco (Fra) Derbi 2:08.503
3. Sandro Cortese (Ger) Aprilia 2:08.638