The session was briefly red flagged when Pramac Ducati's Hector Barbera, making an early return from a broken leg, suffered a highside with ten minutes remaining and was taken to the medical centre for a check up.

Two wild-card CRT entries are present this weekend: Steve Rapp (Attack Performance), who took part in the previous Laguna Seca round but failed to qualify, and fellow AMA star Aaron Yates, who is making his MotoGP debut for GPTech.

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1. Casey Stoner AUS Repsol Honda (RC213V) 1m 41.925s
2. Dani Pedrosa ESP Repsol Honda (RC213V) 1m 42.106s
3. Nicky Hayden USA Ducati Team (GP12) 1m 42.472s
4. Ben Spies USA Yamaha Factory Racing (YZR-M1) 1m 42.536s
5. Stefan Bradl GER LCR Honda MotoGP (RC213V) 1m 43.027s
6. Alvaro Bautista ESP San Carlo Honda Gresini (RC213V) 1m 43.195s
7. Cal Crutchlow GBR Monster Yamaha Tech 3 (YZR-M1) 1m 43.295s
8. Jorge Lorenzo ESP Yamaha Factory Racing (YZR-M1) 1m 43.312s
9. Valentino Rossi ITA Ducati Team (GP12) 1m 43.345s
10. Hector Barbera ESP Pramac Racing (GP12) 1m 43.736s
11. Andrea Dovizioso ITA Monster Yamaha Tech 3 (YZR-M1) 1m 43.745s
12. Yonny Hernandez COL Avintia Blusens (FTR-Kawasaki CRT) 1m 44.328s
13. Aleix Espargaro ESP Power Electronics Aspar (ART CRT) 1m 44.714s
14. Karel Abraham CZE Cardion AB Motoracing (GP12) 1m 44.739s
15. Mattia Pasini ITA Speed Master (ART CRT) 1m 44.913s
16. Randy De Puniet FRA Power Electronics Aspar (ART CRT) 1m 46.298s
17. Ivan Silva ESP Avintia Blusens (FTR-Kawasaki CRT) 1m 46.332s
18. Michele Pirro ITA San Carlo Honda Gresini (FTR-Honda CRT) 1m 46.480s
19. Colin Edwards USA NGM Forward Racing (Suter-BMW CRT) 1m 46.520s
20. Steve Rapp USA Attack Performance (APR-Kawasaki CRT) 1m 46.619s
21. Danilo Petrucci ITA Came IodaRacing (Ioda-Aprilia CRT) 1m 46.941s
22. James Ellison GBR Paul Bird Motorsport (ART CRT) 1m 47.506s
23. Aaron Yates USA GPTech (BCL-Suzuki CRT) 1m 48.054s

Official Indianapolis MotoGP records: Best lap: Casey Stoner AUS Honda 1m 38.850s (2011) Fastest race lap: Casey Stoner AUS Honda 1m 39.807s (2011)