Stefan Bradl claimed his first pole position since Assen in June after a tense battle with championship rival Marc Marquez at Misano.
Marquez had set much of the early running, with 23 minutes to go dropped his bike at Turn 2 just moments after Bradl had displaced him at the top.
As Marquez returned to the pits Bradl set a succession of fastest laps, culminating in a 1m37.507s effort two minutes from the chequered flag.
There was time for Marquez to respond and on his final tour he was faster in the final sector, but eventually fell away and had to settle for second, 0.256s down.
Gresini's Yuki Takahashi improved throughout the session to claim the final spot on the front row, a further quarter of a second down the road from Marquez.
Scott Redding put his Marc VDS Suter fourth on his final tour of Misano, demoting JIR Motobi rider Alex de Angelis into fifth.
Fellow Briton Bradley Smith (Tech 3) was also a late improver as he jumped into sixth as the flag fell, nine thousandths of a second ahead of Andrea Iannone (Speed Master Suter).
Behind Michele Pirro (Gresini), Pol Espargaro finished ninth fastest for HP Tuenti. Older brother Aleix (Pons Kalex) was 12th, with Thomas Luthi (Interwetten) and Jules Cluzel (Forward Suter) splitting the pair.
Pos Rider Team/Bike Time Gap 1. Stefan Bradl Kiefer Kalex 1m37.828s 2. Marc Marquez Catalunya Suter 1m38.084s + 0.256s 3. Yuki Takahashi Gresini Moriwaki 1m38.340s + 0.512s 4. Scott Redding Marc VDS Suter 1m38.364s + 0.536s 5. Alex de Angelis JIR Motobi 1m38.461s + 0.633s 6. Bradley Smith Tech 3 1m38.535s + 0.707s 7. Andrea Iannone Speed Master Suter 1m38.544s + 0.716s 8. Michele Pirro Gresini Moriwaki 1m38.600s + 0.772s 9. Pol Espargaro Speed Up FTR 1m38.647s + 0.819s 10. Thomas Luthi Interwetten Suter 1m38.657s + 0.829s 11. Jules Cluzel Forward Suter 1m38.730s + 0.902s 12. Aleix Espargaro Pons Kalex 1m38.785s + 0.957s 13. Mattia Pasini Ioda FTR 1m38.883s + 1.055s 14. Julian Simon Aspar Suter 1m38.887s + 1.059s 15. Simone Corsi Ioda FTR 1m39.005s + 1.177s 16. Esteve Rabat Blusens FTR 1m39.152s + 1.324s 17. Max Neukirchner MZ 1m39.166s + 1.338s 18. Mike di Meglio Tech 3 1m39.239s + 1.411s 19. Randy Krummenacher Kiefer Kalex 1m39.411s + 1.583s 20. Claudio Corti Italtrans Suter 1m39.432s + 1.604s 21. Alex Baldolini Pons Kalex 1m39.436s + 1.608s 22. Raffaele de Rosa Forward Suter 1m39.440s + 1.612s 23. Xavier Simeon Tech 3 1m39.564s + 1.736s 24. Anthony West MZ 1m39.570s + 1.742s 25. Robertino Pietri Italtrans Suter 1m39.685s + 1.857s 26. Mika Kallio Marc VDS Suter 1m39.701s + 1.873s 27. Ricard Cardus QMMF Moriwaki 1m39.726s + 1.898s 28. Tomoyoshi Koyama Technomag-CIP Suter 1m39.774s + 1.946s 29. Dominique Aegerter Technomag-CIP Suter 1m40.013s + 2.185s 30. Alessandro Andreozzi Andreozzi Corse 1m40.363s + 2.535s 31. Joan Olive Blusens FTR 1m40.459s + 2.631s 32. Santiago Hernandez SAG FTR 1m40.474s + 2.646s 33. Valentin Debise Speed Up FTR 1m40.538s + 2.710s 34. Ratthapak Wilairot SAG FTR 1m40.606s + 2.778s 35. Carmelo Morales La Torre Moriwaki 1m40.607s + 2.779s 36. Jordi Torres Aspar Suter 1m40.821s + 2.993s 37. Kenny Noyes Avintia FTR 1m41.339s + 3.511s 38. Jake Gagne GP Tech FTR 1m41.540s + 3.712s 39. Mashel Al Naimi QMMF Moriwaki 1m41.840s + 4.012s