Jorge Lorenzo took pole position at Laguna Seca but suffered a heavy crash in the closing stages that forced him to be stretchered off the track.
The Yamaha rider, having set the fastest time of 1m21.678s with 12 minutes left in the one-hour session, was thrown off his M1 bike in a high-side at Turn 10 with just three minutes remaining, and landed heavily on his right side.
Curiously, the Spaniard had already crashed at the same spot twenty minutes earlier, when he lost the front and was forced to run back to the pits.
In what turned out to be a surreal end of the session, Casey Stoner also suffered a hard high-side just one minute later, while trying to improve on his second place with his Ducati. The Australian crashed at Turn 3 and was also taken away by stretcher, although initial indications were that he had escaped serious injury.
With the two rivals missing out on the final battle for pole, it was left to championship leader Valentino Rossi to try to get amongst the two at the front, after struggling to be competitive in the final section of the track.
And so he did: when the time had already expired he managed to snatch second away from Stoner, 0.167s behind teammate Lorenzo.
Dani Pedrosa will lead the second row ahead of Honda teammate Andrea Dovizioso, with the other works-spec Honda, Gresini's Toni Elias, in sixth.
Colin Edwards (Tech 3 Yamaha) will lead fellow American Nicky Hayden on the third row, with the Ducati rider scoring his best qualifying result of the year.
The Suzuki pair of Chris Vermeulen and Loris Capirossi round up the top ten.
Pos Rider Bike Time Gap 1. Jorge Lorenzo Yamaha 1m21.678s 2. Valentino Rossi Yamaha 1m21.845s + 0.167s 3. Casey Stoner Ducati 1m21.910s + 0.232s 4. Dani Pedrosa Honda 1m22.113s + 0.435s 5. Andrea Dovizioso Honda 1m22.135s + 0.457s 6. Toni Elias Gresini Honda 1m22.146s + 0.468s 7. Colin Edwards Tech 3 Yamaha 1m22.490s + 0.812s 8. Nicky Hayden Ducati 1m22.540s + 0.862s 9. Chris Vermeulen Suzuki 1m22.633s + 0.955s 10. Loris Capirossi Suzuki 1m22.662s + 0.984s 11. Marco Melandri Hayate Kawasaki 1m22.842s + 1.164s 12. Alex de Angelis Gresini Honda 1m23.004s + 1.326s 13. Sete Gibernau Hernando Ducati 1m23.106s + 1.428s 14. Randy de Puniet LCR Honda 1m23.147s + 1.469s 15. James Toseland Tech 3 Yamaha 1m23.390s + 1.712s 16. Niccolo Canepa Pramac Ducati 1m23.912s + 2.234s 17. Gabor Talmacsi Scot Honda 1m24.528s + 2.850s