Dani Pedrosa edged out MotoGP title rival Jorge Lorenzo to claim pole position at Misano in a session that came alive in the final 10 minutes.
Tech 3's Cal Crutchlow claimed the final front row spot, narrowly denying the satellite Hondas of Stefan Bradl and Alvaro Bautista.
Jonathan Rea, in his MotoGP qualifying debut, meanwhile sealed ninth, just 1.5 seconds down on Pedrosa.
With the field starved of mileage during three practice sessions in which conditions made running almost futile, the opening half of qualifying was unsurprisingly devoted to testing runs and garage feedback rather than chasing times.
That all changed in the final minutes however as times tumbled and the top spot changed hands several times per lap.
With three minutes to go Bradl held provisional pole for his LCR outfit, which is based in San Marino.
Crutchlow snatched pole less than forty seconds later however, before lowering his own benchmark next time around by dipping to a 1m34.001s.
He ran wide on his final lap though, meaning he was powerless to respond if any of his rivals improved.
Fittingly for such a breathless conclusion, he did not have to wait long. Moments after crossing the line, Crutchlow was followed by the works bike of Lorenzo, who set a new overall best of 1m33.875s.
Pedrosa looked well short of matching that but found massive time in the final sector to spring a surprise and claim pole by just 0.018s.
In what was a remarkably close session, Bautista in fifth was still within half a second of Pedrosa's time, while Valentino Rossi - enjoying a strong qualifying in what will be his last race for Ducati on home soil - was 0.7s back in sixth.
Andrea Dovizioso finished seventh ahead of Ben Spies, who had been running well early on but missed the final 10 minute flurry when he dropped his bike at Turn 1.
Pos Rider Team/Bike Time Gap
1. Dani Pedrosa Honda 1m33.857s
2. Jorge Lorenzo Yamaha 1m33.875s + 0.018s
3. Cal Crutchlow Tech 3 Yamaha 1m34.001s + 0.144s
4. Stefan Bradl LCR Honda 1m34.221s + 0.364s
5. Alvaro Bautista Gresini Honda 1m34.299s + 0.442s
6. Valentino Rossi Ducati 1m34.619s + 0.762s
7. Andrea Dovizioso Tech 3 Yamaha 1m34.916s + 1.059s
8. Ben Spies Yamaha 1m34.988s + 1.131s
9. Jonathan Rea Honda 1m35.358s + 1.501s
10. Nicky Hayden Ducati 1m35.401s + 1.544s
11. Karel Abraham Cardion Ducati 1m35.648s + 1.791s
12. Randy de Puniet Aspar Aprilia 1m35.756s + 1.899s
13. Hector Barbera Pramac Ducati 1m36.048s + 2.191s
14. Aleix Espargaro Aspar Aprilia 1m36.284s + 2.427s
15. Michele Pirro Gresini FTR-Honda 1m36.340s + 2.483s
16. James Ellison Paul Bird Aprilia 1m37.124s + 3.267s
17. Mattia Pasini Speed Master Aprilia 1m37.162s + 3.305s
18. Yonny Hernandez Avintia FTR-Kawasaki 1m37.316s + 3.459s
19. Danilo Petrucci Ioda Suter-BMW 1m37.751s + 3.894s
20. Colin Edwards Forward Suter-BMW 1m38.068s + 4.211s
21. David Salom Avintia FTR-Kawasaki 1m40.075s + 6.218s