Jorge Lorenzo was quickest in the race morning warm-up at Indianapolis, while his Yamaha teammate Valentino Rossi suffered his third crash of the weekend.
Having already had accidents in Saturday practice and qualifying, Rossi once again had a low-side fall in the final minutes this morning. The incident happened at low speed and he was able to remount the bike and ride gently back to the pits.
While that left Rossi sixth, Lorenzo put in a last-gasp 1m40.482s lap to knock Dani Pedrosa's Honda off the top spot by 0.226 seconds.
Polesitter Ben Spies (Tech 3 Yamaha) led the way for a while and was third, ahead of Casey Stoner's Ducati and Andrea Dovizioso's Honda. Nicky Hayden, who will start alongside Spies and Lorenzo on the front row, took the second Ducati to seventh.
Pos Rider Team Time Gap
1. Jorge Lorenzo Yamaha 1m40.482s
2. Dani Pedrosa Honda 1m40.708s + 0.226s
3. Ben Spies Tech 3 Yamaha 1m40.711s + 0.229s
4. Casey Stoner Ducati 1m40.804s + 0.322s
5. Andrea Dovizioso Honda 1m40.883s + 0.401s
6. Valentino Rossi Yamaha 1m40.901s + 0.419s
7. Nicky Hayden Ducati 1m41.012s + 0.530s
8. Hector Barbera Aspar Ducati 1m41.261s + 0.779s
9. Marco Melandri Gresini Honda 1m41.303s + 0.821s
10. Alvaro Bautista Suzuki 1m41.545s + 1.063s
11. Mika Kallio Pramac Ducati 1m41.635s + 1.153s
12. Colin Edwards Tech 3 Yamaha 1m41.670s + 1.188s
13. Aleix Espargaro Pramac Ducati 1m41.766s + 1.284s
14. Marco Simoncelli Gresini Honda 1m41.820s + 1.338s
15. Randy de Puniet LCR Honda 1m41.973s + 1.491s
16. Hiroshi Aoyama Interwetten Honda 1m42.016s + 1.534s
17. Loris Capirossi Suzuki 1m42.509s + 2.027s