Jorge Lorenzo claimed his fourth straight pole despite causing a red flag when his engine erupted mid-qualifying, while his Yamaha teammate Valentino Rossi took fifth for his comeback race in Germany.
Lorenzo's engine appeared to detonate on the pit straight just after halfway through the session, with a cloud of smoke, oil and flame trailing the Yamaha until Lorenzo pulled off on an escape road approaching the first corner.
The oil trail then caught out both Ben Spies and Randy de Puniet, who crashed at high speed as they hit the slippery surface, with LCR Honda rider de Puniet clouting Spies' crashed Tech 3 Yamaha with his legs as he tumbled through the gravel.
The Frenchman was removed from the scene on a stretcher and although he was able to return to the LCR garage, he was in too much pain to continue with the session. He has been cleared to race tomorrow however, having escaped with bruising.
It took nearly 25 minutes to clear up after the incident before qualifying could resume. Lorenzo then went into the closing stages third behind Dani Pedrosa (Honda) and Casey Stoner (Ducati), before jumping to the top spot with a 1m21.825s lap - despite encountering Aleix Espargaro's Pramac Ducati along the way.
Lorenzo then trimmed another 0.008sec from his benchmark next time around to cement his pole, with Stoner improving to second, 0.024sec off pole and a tenth ahead of Pedrosa.
Andrea Dovizioso put the second Honda on row two ahead of Rossi's Yamaha. The former champion rode steadily at first and was only 13th following the initial runs, before leaping into the top five for his first race since breaking his leg at Mugello six weeks ago.
Hector Barbera was another sensation of the afternoon, taking his Aspar Ducati to sixth - the best starting position of both his and his team's short MotoGP careers.
De Puniet had been fifth when he crashed and still held on to seventh. The Gresini Hondas of Marco Simoncelli and Marco Melandri were eighth and 10th, split by Espargaro. Spies was only 13th after his crash, but still beat the struggling Suzukis and Ducati's Nicky Hayden.
Alex de Angelis had a substantial accident on the Interwetten Honda with six minutes to go and will start last - although he was unhurt and even made it back out on his spare bike after a speedy jog back to the pits.
Pos Rider Team Time Gap
1. Jorge Lorenzo Yamaha 1m21.817s
2. Casey Stoner Ducati 1m21.841s + 0.024s
3. Dani Pedrosa Honda 1m21.948s + 0.131s
4. Andrea Dovizioso Honda 1m22.263s + 0.446s
5. Valentino Rossi Yamaha 1m22.395s + 0.578s
6. Hector Barbera Aspar Ducati 1m22.454s + 0.637s
7. Randy de Puniet LCR Honda 1m22.610s + 0.793s
8. Marco Simoncelli Gresini Honda 1m22.624s + 0.807s
9. Aleix Espargaro Pramac Ducati 1m22.910s + 1.093s
10. Marco Melandri Gresini Honda 1m22.917s + 1.100s
11. Mika Kallio Pramac Ducati 1m22.961s + 1.144s
12. Colin Edwards Tech 3 Yamaha 1m23.026s + 1.209s
13. Ben Spies Tech 3 Yamaha 1m23.028s + 1.211s
14. Loris Capirossi Suzuki 1m23.040s + 1.223s
15. Nicky Hayden Ducati 1m23.090s + 1.273s
16. Alvaro Bautista Suzuki 1m23.193s + 1.376s
17. Alex de Angelis Interwetten Honda 1m23.515s + 1.698s