Marc Marquez resisted a strong challenge from the Ducatis of Andrea Dovizioso and Andrea Iannone in Brno MotoGP qualifying, as Yamaha had a troubled session.
At a track that had been tipped as one of its best opportunities to unseat Marquez and Honda, Yamaha's first blow came when Valentino Rossi had a violent crash in practice four, falling moments before Alvaro Bautista did likewise at the same spot.
Rossi, who still ended the session fastest, required a precautionary x-ray on his left hand in the medical centre before being cleared to ride again. He did not suffer any broken bones, but did sustain a nasty cut to his little finger.
While Rossi was in pain, his team-mate Jorge Lorenzo had to make a mid-Q2 bike swap as an experimental front brake proved unsuccessful. Only a last-gasp lap got him up from 11th to sixth, one place ahead of Rossi.
With Yamaha struggling, Ducati emerged as Marquez's main threat.
Marquez had taken provisional pole early in Q2, but was then unseated by Pramac rider Iannone in the closing minutes.
The world champion's first reply could only get him to within 0.003 seconds of the satellite Ducati man, although Marquez then claimed pole back with a 1m55.585s.
Iannone could not respond, and was edged out of second by factory Ducati counterpart and 2015 team-mate Dovizioso, who slipped ahead by 0.012s. That still gave Ducati two bikes on the front row.
As had been the case in practice, Tech 3's Bradley Smith was the top Yamaha, thrusting himself ahead of Dani Pedrosa's Honda for fourth with his last lap.
Stefan Bradl and Yonny Hernandez made it through from Q1 to take eighth and 12th on the grid, sandwiching the Espargaro brothers and Cal Crutchlow.
Scott Redding couldn't repeat his Indianapolis Q2 appearance, due in part to a fall at the end of the practice session. He was fifth in Q1, just behind Gresini team-mate Bautista's Factory-spec bike.
Mike di Meglio failed to set a qualifying time at all after crashing both his bikes - one in practice four and one at the start of Q1.
That wasn't what the Avintia crew needed after two accidents from di Meglio's team-mate Hector Barbera earlier in the weekend.
Britain's Leon Camier will start 18th for his second appearance standing in for Nicky Hayden at Aspar, while Colin Edwards' Forward replacement Alex de Angelis will begin his MotoGP return from 20th on the grid.
Pos Rider Team/Bike Time Gap 1. Marc Marquez Honda 1m55.585s 2. Andrea Dovizioso Ducati 1m55.714s +0.129s 3. Andrea Iannone Pramac Ducati 1m55.726s +0.141s 4. Bradley Smith Tech 3 Yamaha 1m55.730s +0.145s 5. Dani Pedrosa Honda 1m55.812s +0.227s 6. Jorge Lorenzo Yamaha 1m55.815s +0.230s 7. Valentino Rossi Yamaha 1m55.821s +0.236s 8. Stefan Bradl LCR Honda 1m55.871s +0.286s 9. Pol Espargaro Tech 3 Yamaha 1m55.899s +0.314s 10. Aleix Espargaro Forward Yamaha 1m56.090s +0.505s 11. Cal Crutchlow Ducati 1m56.129s +0.544s 12. Yonny Hernandez Pramac Ducati 1m56.622s +1.037s 13. Michele Pirro Ducati 1m57.093s Q1 14. Alvaro Bautista Gresini Honda 1m57.428s Q1 15. Scott Redding Gresini Honda 1m57.557s Q1 16. Hiroshi Aoyama Aspar Honda 1m57.984s Q1 17. Karel Abraham Cardion Honda 1m58.100s Q1 18. Leon Camier Aspar Honda 1m58.935s Q1 19. Danilo Petrucci Ioda Aprilia 1m58.863s Q1 20. Alex de Angelis Forward Yamaha 1m58.948s Q1 21. Hector Barbera Avintia FTR-Kawasaki 1m58.968s Q1 22. Michael Laverty PBM-Aprilia 1m58.968s Q1 23. Broc Parkes PBM-Aprilia 1m59.581s Q1 24. Mike di Meglio Avintia FTR-Kawasaki no time Q1