Cal Crutchlow captured only the second pole of his MotoGP career, setting a new lap record at the Brno circuit.
The Briton prevailed in a frantic session that threw up plenty of surprises, not least in the performance of satellite Honda rider Alvaro Bautista.
The Spaniard moved onto provisional pole for Gresini with a lap record of his own after the opening set of runs.
His time would have been good enough for pole but for Tech 3's Crutchlow, who blazed to an emphatic 1m55.527s on his first run on fresh rubber.
There was still three minutes for the usual suspects to usurp him, and several times Marc Marquez and Jorge Lorenzo threatened to do so, matching the Briton through the first sector.
They could not keep it up over the remainder of the lap however, leaving Crutchlow free to claim pole.
Bautista's best was good enough for second, while Marquez hung onto third ahead of works Honda team-mate Dani Pedrosa.
Lorenzo was fifth, while Bradley Smith scored another satellite upset as he beat works Yamaha counterpart Valentino Rossi to sixth.
Stefan Bradl, Andrea Dovizioso and Nicky Hayden rounded out the top 10.
Andrea Iannone and Colin Edwards made it through into Q2 after an equally frenetic first shootout.
Iannone crashed on his out-lap, but with three minutes on the clock made it back to his garage, ran onto a spare bike and headed out with time for one flyer, which was enough to lift him into 11th.
Edwards meanwhile held off Aleix Espargaro to claim 12th, and give his Forward Racing squad only its second Q2 berth.
Pos Rider Team/Bike Time Gap 1. Cal Crutchlow Tech 3 Yamaha 1m55.527s 2. Alvaro Bautista Gresini Honda 1m55.754s +0.227s 3. Marc Marquez Honda 1m55.863s +0.336s 4. Dani Pedrosa Honda 1m55.868s +0.341s 5. Jorge Lorenzo Yamaha 1m55.949s +0.422s 6. Bradley Smith Tech 3 Yamaha 1m56.014s +0.487s 7. Valentino Rossi Yamaha 1m56.186s +0.659s 8. Stefan Bradl LCR Honda 1m56.477s +0.950s 9. Andrea Dovizioso Ducati 1m56.825s +1.298s 10. Nicky Hayden Ducati 1m56.979s +1.452s 11. Andrea Iannone Pramac Ducati 1m57.455s +1.928s 12. Colin Edwards Forward FTR-Kawasaki 1m58.392s +2.865s 13. Aleix Espargaro Aspar Aprilia 1m58.378s +2.851s 14. Michele Pirro Pramac Ducati 1m58.812s +3.285s 15. Randy de Puniet Aspar Aprilia 1m58.953s +3.426s 16. Yonny Hernandez PBM Aprilia 1m58.983s +3.456s 17. Danilo Petrucci Ioda-Suter-BMW 1m59.057s +3.530s 18. Claudio Corti Forward FTR-Kawasaki 1m59.062s +3.535s 19. Hector Barbera Avintia FTR-Kawasaki 1m59.128s +3.601s 20. Lukas Pesek Ioda-Suter-BMW 2m00.522s +4.995s 21. Michael Laverty PBM-Aprilia 2m00.584s +5.057s 22. Hiroshi Aoyama Avintia FTR-Kawasaki 2m00.653s +5.126s 23. Karel Abraham Cardion Aprilia 2m00.792s +5.265s 24. Bryan Staring Gresini FTR-Honda 2m00.827s +5.300s 25. Martin Bauer Remus Aprilia 2m01.135s +5.608s