Australian Stoner finished the season is style with his sixth victory
Casey Stoner cruised to victory in the final MotoGP race of the season in Valencia, while Valentino Rossi came third to set a new points total record.
World champion Rossi started 10th on the grid but clinched a podium place to end the season with 373 points, beating the previous best of 367.
Jorge Lorenzo came home in eighth to win the "rookie of the year" title ahead of Andrea Dovizioso.
Dovizioso's fourth place was not enough to make up the points gap on his rival.
Britain's James Toseland suffered a frustrating end to his first season in MotoGP as he slipped from fifth place on the starting grid to finish 11th.
Australian Stoner streaked away from pole position on his Ducati after recovering from a sluggish start when he was briefly overtaken by Pedrosa.
Rossi showed remarkable form to charge through the field, from the fourth row of the grid after a poor qualifying performance, to clinch his 16th podium finish in 18 races.
Valencia MotoGP result:
1. Casey Stoner (Australia) Ducati 46 mins 46.114 secs
2. Dani Pedrosa (Spain) Honda 46:49.504
3. Valentino Rossi (Italy) Yamaha 46:58.308
4. Andrea Dovizioso (Italy) Honda 47:10.273
5. Nicky Hayden (U.S.) Honda 47:12.346
6. Colin Edwards (U.S.) Yamaha 47:18.323
7. Shinya Nakano (Japan) Honda 47:20.685
8. Jorge Lorenzo (Spain) Yamaha 47:21.775
9. Loris Capirossi (Italy) Suzuki 47:24.342
10. Alex de Angelis (San Marino) Honda 47:33.697
World championship standings:
1 V Rossi (Ita) Yamaha 373 points * world champion
2 C Stoner (Aus) Ducati 280
3 D Pedrosa (Spn) Honda 249
4 J Lorenzo (Spn) Yamaha 190
5 A Dovizioso (Ita) Honda 175
6 N Hayden (US) Honda 155
7 C Edwards (US) Yamaha 144
8 C Vermeulen (Aus) Suzuki 128
9 S Nakano (Jpn) Honda 126
10 L Capirossi (Ita) Suzuki 118
250cc race result:
1. Marco Simoncelli, Italy, Gilera, 43 minutes, 29.003 seconds.
2. Yuki Takahashi, Japan, Honda, 43:34.167.
3. Alvaro Bautista, Spain, Aprilia, 43:37.651.
250cc championship standings:
1 M Simoncelli (Ita) Gilera 281 points * world champion
2 A Bautista (Spn) Aprilia 244
3 M Kallio (Fin) KTM 196
125cc race result:
1. Simone Corsi, Italy, Aprilia, 40 minutes, 45.715 seconds.
2. Nicolas Terol, Spain, Aprilia, 40:45.821.
3. Mike Di Meglio, France, Derbi, 40:45.938.
125cc championship standings:
1 M di Meglio (Fra) Derbi 264 points
2 S Corsi (Ita) Aprilia 225
3 G Talmacsi (Hng) Aprilia 206