Stoner is aiming for a third consecutive win this season, having won the previous races at Donington and Assen.
He will also hope to make amends for last season's fifth place finish here after he had started the race on pole, and admitted the weather would be a big factor in how the day went.
"We have a decision to make on the race tyre depending on the weather because track temperature in qualifying was about 15 degrees less than the day before, so the hard compounds we were using just struggled a little bit," he said.
"We couldn't do quite the same lap times although I wasn't pushing as hard either, so it would make the decision easier if the sun comes back out for the race."
Rossi said an incident with team-mate Lorenzo had hampered his chances.
"He was slowing down to enter the pits and he didn't see me, this was just unlucky because I think that lap could have been good enough for the second row," he said.
"Then with my last tyre my lap looked like it would be good enough for the front row but I had some problems with grip on the last two corners and I lost about half a second."
German MotoGP qualifying result:
1 C Stoner (Aus) Ducati 1:21.067 2 D Pedrosa (Sp) Honda 1:21.420 3 C Edwards (US) Tech 3 Yamaha 1:21.519 4 A Dovizioso (It) JiR Honda 1:21.656 5 J Lorenzo (Sp) Fiat Yamaha 1:21.795 6 R de Puniet (Fr) LCR Honda 1:21.821 7 V Rossi (It) Fiat Yamaha 1:21.845 8 N Hayden (US) Repsol Honda 1:21.876 9 S Nakano (Jpn) Gresini Honda 1:21.920 10 A de Angelis (SM) Gresini Honda 1:21.977
250cc qualifying result:
1 M Simoncelli (It) Gilera 1:23.399 2 J Simon (Sp) KTM 1:24.057 3 H Barbera (Sp) Aprilia 1:24.077
125cc qualifying result:
1 G Talmacsi (Hng), Aprilia 1:27.552 2 B Smith (GB) Aprilia 1:27.645 3 S Bradl (Ger) Aprilia 1:27.921
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