Jorge Lorenzo beat star independent rider Randy de Puniet to Silverstone pole, while third-placed Dani Pedrosa had a big accident at the end of the session.
De Puniet was the sensation of qualifying, putting his LCR Honda on provisional pole and extending the margin shortly afterward.
As the big names tried and failed to depose him, it looked increasingly likely that de Puniet would be the first non-factory polesitter since Casey Stoner took a pole for the same squad in early 2006.
Lorenzo (Yamaha) trailed de Puniet's time until the final sector of his best lap, when he found a vast improvement to knock the Frenchman off pole – and claim his first of the year.
De Puniet's last bid to take the position back ended with a crash in the Arena section, from which he quickly walked away.
But Pedrosa needed medical assistance when he fell at Brooklands moments earlier. The Honda rider had difficulty getting up after the accident and was eventually taken away by stretcher. His bike continued head-on into the barriers and was substantially damaged.
Andrea Dovizioso put the second Honda fourth, ahead of the two Ducatis – Nicky Hayden ahead of Casey Stoner.
Tech 3 Yamaha duo Ben Spies and Colin Edwards were seventh and 10th, split by the Gresini Hondas, while Suzuki's tough weekend continued as Loris Capirossi and Alvaro Bautista qualified back in 14th and 15th.
Pos Rider Team Time Gap
1. Jorge Lorenzo Yamaha 2m03.308s
2. Randy de Puniet LCR Honda 2m03.434s + 0.126s
3. Dani Pedrosa Honda 2m03.586s + 0.278s
4. Andrea Dovizioso Honda 2m03.995s + 0.687s
5. Nicky Hayden Ducati 2m04.334s + 1.026s
6. Casey Stoner Ducati 2m04.394s + 1.086s
7. Ben Spies Tech 3 Yamaha 2m04.477s + 1.169s
8. Marco Melandri Gresini Honda 2m04.555s + 1.247s
9. Marco Simoncelli Gresini Honda 2m04.868s + 1.560s
10. Colin Edwards Tech 3 Yamaha 2m05.035s + 1.727s
11. Hector Barbera Aspar Ducati 2m05.354s + 2.046s
12. Hiroshi Aoyama Interwetten Honda 2m05.712s + 2.404s
13. Aleix Espargaro Pramac Ducati 2m05.748s + 2.440s
14. Loris Capirossi Suzuki 2m05.821s + 2.513s
15. Alvaro Bautista Suzuki 2m06.607s + 3.299s
16. Mika Kallio Pramac Ducati 2m06.980s + 3.672s