Marc Marquez fell while fastest with four minutes remaining, with Stefan Bradl then snatching his first MotoGP pole from the absent Marquez in the final minute.
Cal Crutchlow battled technical problems throughout the session and only set a lap time in the closing minutes.
Title contenders Dani Pedrosa and Jorge Lorenzo are returning from collarbone injuries sustained during practice for last weekend's German round.
Andrea Iannone has been ruled out after dislocating his shoulder at the Sachsenring and is not replaced. Iannone's long-injured Pramac Ducati team-mate Ben Spies is being replaced by Moto2 rider Alex de Angelis.
American Blake Young was due to make his second wild-card appearance of the year with Attack Performance Racing, but withdrew after heavy damage to the bike on Friday.
for pictures from the grand prix...
1. Stefan Bradl
GER LCR Honda MotoGP (RC213V) 1m 21.176s
2. Marc Marquez
ESP Repsol Honda Team (RC213V) 1m 21.193s
3. Alvaro Bautista
ESP Go&Fun Honda Gresini (RC213V) 1m 21.373s
4. Valentino Rossi
ITA Yamaha Factory Racing (YZR-M1) 1m 21.418s
5. Cal Crutchlow
GBR Monster Yamaha Tech 3 (YZR-M1) 1m 21.420s
6. Jorge Lorenzo
ESP Yamaha Factory Racing (YZR-M1) 1m 21.453s
7. Dani Pedrosa
ESP Repsol Honda Team (RC213V) 1m 21.728s
8. Andrea Dovizioso
ITA Ducati Team (GP13) 1m 22.026s
9. Bradley Smith
GBR Monster Yamaha Tech 3 (YZR-M1) 1m 22.075s
10. Nicky Hayden
USA Ducati Team (GP13) 1m 22.090s
11. Aleix Espargaro
ESP Power Electronics Aspar (ART CRT) 1m 22.099s
12. Randy De Puniet
FRA Power Electronics Aspar (ART CRT) No Time
13. Hector Barbera
ESP Avintia Blusens (FTR-Kawasaki CRT)* 1m 22.808s
14. Alex De Angelis
RSM Ignite Pramac Racing (GP13) 1m 23.253s
15. Colin Edwards
USA NGM Forward Racing (FTR-Kawasaki CRT)* 1m 23.272s
16. Danilo Petrucci
ITA Came IodaRacing Project (Suter-BMW CRT)* 1m 23.323s
17. Claudio Corti
ITA NGM Forward Racing (FTR-Kawasaki CRT)* 1m 23.616s
18. Yonny Hernandez
COL Paul Bird Motorsport (ART CRT) 1m 23.875s
19. Karel Abraham
CZE Cardion AB Motoracing (ART CRT) 1m 23.919s
20. Michael Laverty
GBR Paul Bird Motorsport (PBM-ART CRT)* 1m 23.987s
21. Hiroshi Aoyama
JPN Avintia Blusens (FTR-Kawasaki CRT)* 1m 24.235s
22. Bryan Staring
AUS Go&Fun Honda Gresini (FTR-Honda CRT) 1m 24.756s
23. Lukas Pesek
CZE Came IodaRacing Project (Suter-BMW CRT)* 1m 24.809s
* Standard ECU.
Fastest practice time:
ESP Honda 1m 21.568s
Official Laguna Seca MotoGP records:
ESP Yamaha 1m 20.554
Fastest race lap:
ESP Honda 1m 21.229s
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