Pol Espargaro captured his seventh pole of this year's Moto2 campaign despite a violent late fall at Valencia.
The Spaniard had been almost half a second clear of the field when he went down heavily on the exit of Turn 4, bringing his session to a premature conclusion 12 minutes from the end.
Despite missing the late running, Espargaro's best of 1m35.191s proved enough to hang on to pole for the final race of the season.
In the end that proved no influence on the pole fight however, with the Monlau Suter man unable to match Espargaro.
Marquez also fell five minutes from the end, but was able to get his bike restarted and even improved on his final lap - although he was still more than four tenths off pole.
No other rider was able to get within half a second of the benchmark time, with Thomas Luthi - third in the session and therefore second on Sunday's grid - 0.565s in arrears.
The Swiss rider can still catch Andrea Iannone, who starts from ninth, for third place in the championship.
Takaaki Nakagami claimed the final share of the front row, with Nico Terol, Jordi Torres and Dominique Aegerter rounding out the top six.
In what was a relatively low-key session, Scott Redding claimed seventh ahead of Simone Corsi and Iannone.
Bradley Smith was only 22nd in his final Moto2 qualifying session before stepping up to the Tech3 MotoGP squad.
Pos Rider Team/Bike Time Gap 1. Pol Espargaro Pons Kalex 1m35.191s 2. Marc Marquez Monlau Suter 1m35.597s + 0.406s 3. Thomas Luthi Paddock Suter 1m35.756s + 0.565s 4. Takaaki Nakagami Italtrans Kalex 1m35.801s + 0.610s 5. Nicolas Terol Aspar Suter 1m35.858s + 0.667s 6. Jordi Torres Aspar Suter 1m35.915s + 0.724s 7. Dominique Aegerter Technomag-CIP Suter 1m35.949s + 0.758s 8. Scott Redding Marc VDS Kalex 1m35.966s + 0.775s 9. Simone Corsi Ioda FTR 1m35.983s + 0.792s 10. Andrea Iannone Speed Master Speed Up 1m36.016s + 0.825s 11. Johann Zarco JIR Motobi 1m36.108s + 0.917s 12. Julian Simon Avintia Suter 1m36.129s + 0.938s 13. Xavier Simeon Tech 3 1m36.236s + 1.045s 14. Esteve Rabat Pons Kalex 1m36.278s + 1.087s 15. Toni Elias Italtrans Kalex 1m36.483s + 1.292s 16. Mika Kallio Marc VDS Kalex 1m36.489s + 1.298s 17. Mike di Meglio Kiefer Kalex 1m36.511s + 1.320s 18. Yuki Takahashi Forward FTR 1m36.583s + 1.392s 19. Randy Krummenacher Switzerland Kalex 1m36.629s + 1.438s 20. Gino Rea Gresini Suter 1m36.687s + 1.496s 21. Roman Ramos SAG FTR 1m36.701s + 1.510s 22. Bradley Smith Tech 3 1m36.771s + 1.580s 23. Mattia Pasini Forward FTR 1m36.868s + 1.677s 24. Ratthapark Wilairot Gresini Suter 1m36.873s + 1.682s 25. Marcel Schrotter SAG Bimota 1m36.990s + 1.799s 26. Axel Pons Pons Kalex 1m37.096s + 1.905s 27. Dani Rivas TSR Kalex 1m37.228s + 2.037s 28. Tomoyoshi Koyama Technomag-CIP Suter 1m37.357s + 2.166s 29. Ricard Cardus Arguinano AJR 1m37.384s + 2.193s 30. Alessandro Andreozzi Speed Master Speed Up 1m37.463s + 2.272s 31. Rafid Topan Sucipto QMMF Speed Up 1m38.982s + 3.791s 32. Eric Granado JIR Motobi 1m39.602s + 4.411s 33. Elena Rosell QMMF Speed Up 1m40.063s + 4.872s