Valentino Rossi's brave decision to take part in the season-ending Valencia Grand Prix was ruined when an engine failure forced him out of the race.
Rossi had to settle for third place in the final standings
The Yamaha rider, who broke three bones in his hand in Saturday's qualifying, lost second place in the Championship to Dani Pedrosa as a result.
Honda's Pedrosa started on pole and won the race by more than five seconds from new champion Casey Stoner.
Rossi had not finished outside the top two in any category since 1996.
That was when he came ninth in the 125cc in what was his first season.
"I am very happy, I didn't expect this," Pedrosa told BBC Sport. It made the Spaniard the first rider to win in all three classes in Valencia.
Stoner finished top of the final standings with 367 points after winning 10 of the 18 races on his Ducati. Pedrosa was second on 242 with Rossi third on 241.
Suzuki rider John Hopkins was fourth in the overall standings after finishing third in Valencia.
Although Pedrosa started on pole for the fourth successive race Stoner overtook him off the grid but the Spaniard regained the lead on the sixth lap and never relinquished it.
Rossi started the race in second-last place but managed to work his way into a points-scoring position before being forced to stop with 11 laps remaining.
1. Dani Pedrosa (Spain) Honda 46 minutes, 43.533 seconds
2. Casey Stoner (Australia) Ducati 46:48.980
3. John Hopkins (US) Suzuki 47:03.937
4. Marco Melandri (Italy) Honda 47:08.360
5. Loris Capirossi (Italy) Ducati 47:09.337
6. Chris Vermeulen (Australia) Suzuki 47:09.395
7. Alex Barros (Brazil) Ducati 47:13.003
8. Nicky Hayden (US) Honda 47:13.866
9. Randy de Puniet (France) Kawasaki 47:14.428
10. Toni Elias (Spain) Honda 47:14.563
Final championship standings:
1. Casey Stoner (Australia) Ducati 367 points
2. Dani Pedrosa (Spain) Honda 242
3. Valentino Rossi (Italy) Yamaha 241
4. John Hopkins (US) Suzuki 189
5. Marco Melandri (Italy) Honda 187
6. Chris Vermeulen (Australia) Suzuki 179
7. Loris Capirossi (Italy) Ducati 166
8. Nicky Hayden (US) Honda 127
9. Colin Edwards (US) Yamaha 124
10. Alex Barros (Brazil) Ducati 115