Leon Camier had been leading until the end of the session, but Smrz struck late to deny him a first Superbike Championship pole position.
The previous practice session had been dry, but a deluge changed the competition ahead of the Superpole, which was declared as wet and split into two 20-minute sessions.
Davide Giugliao, Carlos Checa and Tom Sykes all suffered crashes which ended their afternoons, which left five final riders gunning for the top slot.
Leon Haslam made it two Brits on the front row with fourth place, while Sylvain Guintoli marked his return to Superbikes in the PATA Ducati team with third on the grid.
1. Jakub Smrz CZE Liberty Effenbert Ducati 1098R 2m 20.810s
2. Leon Camier GBR FIXI Crescent Suzuki GSX-R1000 2m 20.846s
3. Sylvain Guintoli FRA PATA Ducati 1098R 2m 21.385s
4. Leon Haslam GBR BMW Motorrad S1000RR 2m 21.613s
5. Davide Giugliano ITA Althea Ducati 1098R 2m 21.951s
6. Marco Melandri ITA BMW Motorrad S1000RR 2m 21.960s
7. Carlos Checa ESP Althea Ducati 1098R 2m 23.356s
8. Tom Sykes GBR Kawasaki Racing ZX-10R 2m 24.025s
9. Loris Baz FRA Kawasaki Racing ZX-10R 2m 23.777s
10. Jonathan Rea GBR Honda WSBK CBR1000RR 2m 23.889s
11. Max Biaggi ITA Aprilia Racing RSV-4 2m 24.176s
12. John Hopkins USA FIXI Crescent Suzuki GSX-R1000 2m 24.274s
13. Maxime Berger FRA Effenbert Liberty Ducati 1098R 2m 24.294s
14. Eugene Laverty IRL Aprilia Racing RSV-4 2m 25.260s
15. Michel Fabrizio ITA BMW Italia Goldbet S1000RR 2m 26.137s
16. Chaz Davies GBR ParkinGO MTC Aprilia RSV-4 2m 26.360s
Did not progress to Superpole
17. Niccolo Canepa ITA Red Devils Ducati 1098R 2m 06.795s
18. Ayrton Badovini ITA BMW Italia Goldbet S1000RR 2m 06.803s
19. Lorenzo Zanetti ITA PATA Ducati 1098R 2m 06.869s
20. Hiroshi Aoyama JPN Honda WSBK CBR1000RR 2m 06.921s
21. David Salom ESP Pedercini Kawasaki ZX-10R 2m 08.069s
22. David Johnson AUS Pedercini Kawasaki ZX-10R 2m 09.762s
23. Norino Brignola ITA Grillini Progea BMW S1000RR 2m 10.912s
24. Brett McCormick CAN Effenbert Liberty Ducati 1098R 2m 13.730s