Afterwards, Stoner said he was glad the weather had not played a big outcome in the race, and admitted fate had been on his side - at last.
"I didn't want to have the weather in the mix, maybe throwing a few spits and spots here and there but it managed to stay clear for the race so I'm pretty happy about that," he said.
"As for Valentino crashing, it's very unfortunate. I don't want to catch up in points that way but I've had my run of bad luck as well from the beginning of the season. So it's time that we started to have some decent results."
Rossi accepted blame for his mistake which took Randy de Puniet out of the race.
"After seven podiums in a row, I made a mistake today - this is racing," he said.
"I arrived too fast when the tyres were still cold, I was too hard on the brakes and I lost the rear.
"I am sincerely sorry to Randy de Puniet and all of his team. After the crash I had a bent handlebar and no gear shifter, but despite this I was able to do the third fastest lap time."
Earlier on, the 125cc race was won by reigning world champion Gabor Talmacsi.
The Hungarian held on to come home ahead of Joan Olive and Simone Corsi at the end of a five-lap race which was forced when the original race was red-flagged for rain.
Briton Bradley Smith had just skidded out from the lead as the red flags went up, so began the re-start from front spot on the grid, but finished the shortened race in fifth.
The 250cc race was won by Alvaro Bautista, ahead of Thomas Luethi and Marco Simoncelli.
Dutch MotoGP race result:
1 C Stoner (Aus) Ducati 42m 12.337 2 D Pedrosa (Spn) Honda 42:23.647 3 C Edwards (US) Yamaha 42:29.462 4 N Hayden (US) Honda 42:32.814 5 A Dovizioso (Ita) Honda 42:39.683 6 J Lorenzo (Spn) Yamaha 42:40.945 7 C Vermeulen (Aus) Suzuki 42:44.667 8 S Nakano (Jpn) Honda 42:47.229 9 J Toseland (GB) Yamaha 42:50.903 10 S Guintoli (Fr) Ducati 42:51.154
11 V Rossi (Ita) Yamaha 42:58.362
World championship standings:
1 D Pedrosa (Sp) Honda 171 pts 2 V Rossi (It) Yamaha 167 3 C Stoner (Aus) Ducati 142 4 J Lorenzo (Sp) Yamaha 114 5 C Edwards (US) Yamaha 98
250cc race result:
1 A Bautista (Spn) Aprilia 40m 54.117 2 T Luethi (Swi) Aprilia 40:58.714 3 M Simoncelli (Ita) Gilera 41:00.120
250cc championship standings:
1 M Kallio (Fin) KTM 140 points 2 M Simoncelli (Ita) Gilera 139 3 A Debon (Spn) Aprilia 114
125cc race result (five laps):
1 G Talmacsi (Hng) Aprilia 9mins 04.520secs 2 J Olive (Spn) Derbi 9:04.648 3 S Corsi (Ita) Aprilia 9:04.775
125cc championship standings:
1 M Di Meglio (France) Derbi 141 points 2 S Corsi (Italy) Aprilia 125 3 J Olive (Spain) Derbi 94
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