Pedrosa trails Lorenzo by 72 points in the riders' standings
Spain's Dani Pedrosa will start in pole position for Sunday's Czech MotoGP after topping qualifying in Brno.
The Repsol Honda rider, second in the rider standings, timed one minute 56.508 seconds to deny rookie Ben Spies his first MotoGP pole by 0.338 seconds.
Yamaha's championship leader Jorge Lorenzo crashed in the final minutes of the session, failing to claim his sixth pole in a row and was third fastest.
Valentino Rossi also came off his bike and will start fifth on the grid.
Both Lorenzo and world champion Rossi, competing in his third grand prix after returning from a four-race absence due to a broken leg, escaped unhurt.
Australia's former world champion Casey Stoner, on a Ducati, managed to claim fourth position.
Spaniard Alvaro Bautista is a doubt to race on Sunday after the Suzuki rider suffered a heavy fall in morning practice.
In the 125cc class, Briton Bradley Smith will start at the front for the first time after a lap of 2:07.146 ended championship frontrunner Marc Marquez's run of four successive poles.
Czech GP qualifying result:
1 Dani Pedrosa (Spn) Honda 1:56.508
2 Ben Spies (US) Yamaha 1:56.846
3 Jorge Lorenzo (Spn) Yamaha 1:56.865
4 Casey Stoner (Aus) Ducati, 1:56.868
5 Valentino Rossi (Ita) Yamaha 1:57.059
6 Andrea Dovizioso (Ita) Honda 1.57.117
7 Colin Edwards (US) Yamaha 1:57.222
8 Nicky Hayden (US) Ducati 1:57.635
9 Hector Barbera (Spn) Ducati 1:57.960
10 Loris Capirossi (Ita) Suzuki, 1:57.981
125cc qualifying result:
1 Bradley Smith (GB) Aprilia 2:07.146
2 Nicolas Terol (Spn) Aprilia 2:07.630
3 Pol Espargaro (Spn) Derbi 2:08.073
More to follow.
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