Aleix Espargaro walked away from a nasty highside out of the final turn, then went to the medical centre to have a hand injury examined. He should return for qualifying.
Stefan Bradl saved a major moment early in the session, but then slid off his LCR Honda in the closing minutes.
Qualifying 1, for those outside the top ten after third free practice, will now get underway.
Pramac Ducati's Ben Spies has been forced to withdraw after dislocating his left shoulder in Saturday morning practice. The luckless Spies has not raced since round two due to right shoulder injuries.
American Blake Young is making his third wild-card appearance of the year this weekend, with Attack Performance Racing.
for pictures from the grand prix...
1. Marc Marquez
ESP Repsol Honda Team (RC213V) 1m 38.986s
2. Cal Crutchlow
GBR Monster Yamaha Tech 3 (YZR-M1) 1m 39.114s
3. Stefan Bradl
GER LCR Honda MotoGP (RC213V) 1m 39.137s
4. Jorge Lorenzo
ESP Yamaha Factory Racing (YZR-M1) 1m 39.317s
5. Dani Pedrosa
ESP Repsol Honda Team (RC213V) 1m 39.500s
6. Alvaro Bautista
ESP Go&Fun Honda Gresini (RC213V) 1m 39.581s
7. Valentino Rossi
ITA Yamaha Factory Racing (YZR-M1) 1m 39.782s
8. Bradley Smith
GBR Monster Yamaha Tech 3 (YZR-M1) 1m 39.978s
9. Andrea Dovizioso
ITA Ducati Team (GP13) 1m 40.171s
10. Nicky Hayden
USA Ducati Team (GP13) 1m 40.373s
11. Andrea Iannone
ITA Energy T.I. Pramac Racing (GP13) 1m 40.881s
12. Claudio Corti
ITA NGM Forward Racing (FTR-Kawasaki CRT)* 1m 41.195s
13. Colin Edwards
USA NGM Forward Racing (FTR-Kawasaki CRT)* 1m 41.215s
14. Danilo Petrucci
ITA Came IodaRacing Project (Suter-BMW CRT)* 1m 41.355s
15. Hector Barbera
ESP Avintia Blusens (FTR-Kawasaki CRT)* 1m 41.594s
16. Yonny Hernandez
COL Paul Bird Motorsport (ART CRT) 1m 41.840s
17. Randy De Puniet
FRA Power Electronics Aspar (ART CRT) 1m 41.844s
18. Michael Laverty
GBR Paul Bird Motorsport (PBM-ART CRT)* 1m 42.113s
19. Hiroshi Aoyama
JPN Avintia Blusens (FTR-Kawasaki CRT)* 1m 42.164s
20. Lukas Pesek
CZE Came IodaRacing Project (Suter-BMW CRT)* 1m 42.231s
21. Bryan Staring
AUS Go&Fun Honda Gresini (FTR-Honda CRT) 1m 42.550s
22. Aleix Espargaro
ESP Power Electronics Aspar (ART CRT) 1m 43.068s
23. Karel Abraham
CZE Cardion AB Motoracing (ART CRT) 1m 43.085s
24. Blake Young
USA Attack Performance Racing (APR-Kawasaki CRT) 1m 45.139s
* Standard ECU.
Fastest practice time:
ESP Honda 1m 38.844s
Official Indianapolis MotoGP records:
ESP Honda 1m 38.813s
Fastest race lap:
ESP Honda 1m 39.088s
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