Michelin riders Dovizioso and Edwards both held podium places during the early part of the race, but had been pushed back to fifth and sixth by the halfway stage - with Edwards then crashing out of fifth on lap 21. Dovizioso, who began the race a career best fourth on the grid, inherited that position and was the only Michelin rider in the top seven.
Sylvain Guintoli made up for a poor 15th in qualifying with a Desmosedici best of sixth in the race, with Loris Capirossi just edging out LCR's Randy de Puniet for seventh position on the second Rizla Suzuki.
de Angelis' Honda Gresini team-mate Shinya Nakano and Anthony West completed the top ten - West, the lone Kawasaki rider in this weekend's event, fighting back from a fall.
Stoner's team-mate Marco Melandri, riding in what is rumoured to be his penultimate race for Ducati, wasn't so fortunate. The Italian climbed from 16th to seventh by lap ten, when he was the fastest man on track, but then promptly crashed out.
Race winning MotoGP rookie Jorge Lorenzo also failed to finish, the Fiat Yamaha rider having been spat from his factory M1 on lap three.
Rounding out the 13 finishers was Pedrosa's team-mate Nicky Hayden. The American was desperately unhappy with his Repsol Honda from the very start and pitted for a new tyre on lap eight.
The two other riders to finish a lap down were James Toseland and Toni Elias, neither of whom looked comfortable in the slippery conditions.
German Grand Prix:
4. de Angelis
8. de Puniet