Pedrosa's Repsol Honda team-mate Andrea Dovizioso featured in the lead group in the early stages, but dropped back with front tyre problems, which eventually forced his retirement - Dovizioso's third DNF in a row.
Alex de Angelis converted his second row start into a season best fifth for San Carlo Honda Gresini, eleven seconds from Stoner and ten in front of team-mate Toni Elias, who stole sixth from Hayate's Marco Melandri after a close battle.
Fourth on the grid Nicky Hayden ran wide at turn one, costing him any chance of a strong result. He brought his factory Ducati home within half a second of Melandri while Monster Tech 3 Yamaha riders Colin Edwards and James Toseland were a closely matched ninth and tenth.
A disappointing weekend fir Rizla Suzuki ended with Loris Capirossi eleventh and Chris Vermeulen 13th, despite the tight Sachsenring looking like a favourable track for the comparatively underpowered GSV-R.
Having survived a spectacular take-out by Hayden in qualifying, Niccolo Canepa was rewarded with a twelfth place finish - as the top rookie - with Pramac Ducati team-mate Mika Kallio dropping back to 14th.
15th and last was fellow rookie Gabor Talmacsi, who claimed his first MotoGP point and the first premier-class point by a Hungarian since Arpad Juhos finished ninth at the East German GP in 1972
Joining Dovizioso on the DNF list was Randy de Puniet, who rose from sixth to third on the opening lap, only to suffer a huge highside from his LCR Honda at the top of the hill later in the lap. The incident marked de Puniet's first race crash of the season.
The MotoGP grid has been reduced to 17 permanent riders following the departure of the Grupo Francisco Hernando team, which had been running Sete Gibernau.
Round ten of the 2009 world championship, the British Grand Prix at Donington Park, takes place next weekend, after which the summer break begins.
German Grand Prix:
5. de Angelis