Wold championship leader Pedrosa missed the second half of the session after a lowside fall from his factory Honda, while holding provisional pole.
Aleix Espargaro regained top CRT honors from Aspar team-mate Randy de Puniet with seventh in qualifying. Gresini Honda's Alvaro Bautista was eighth quickest and de Puniet ninth.
Ducati riders Nicky Hayden and Michele Pirro were left tenth and eleventh, with world champion Jorge Lorenzo absent after breaking his collarbone on Thursday. Lorenzo is on his way back to Assen and may try and ride in Saturday's race.
Marquez is also injured, after suffering fractures to his little finger and toe in Friday morning practice.
Andrea Dovizioso - who joined Ducati team-mate Hayden in Q1 - was not able to progress to the second and final part of qualifying.
1. Cal Crutchlow
2. Marc Marquez
3. Stefan Bradl
4. Valentino Rossi
5. Dani Pedrosa
6. Bradley Smith
7. Aleix Espargaro
8. Alvaro Bautista
9. Randy De Puniet
10. Nicky Hayden
11. Michele Pirro
12. Jorge Lorenzo
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