(CNN) -- Dani Pedrosa led from start to finish to claim victory at his home Valencia Grand Prix to end the MotoGP season in third place overall.
The Spaniard took advantage of pole winner Casey Stoner's crash in the warm-up lap to deny the Australian a top-three finish to the year as he headed off world champion Valentino Rossi to record only his second victory of 2009.
The Repsol Honda rider finished Sunday's race 2.630 seconds ahead of Rossi, who notched his 13th podium placing this year to follow up clinching the title in Malaysia on October 25.
Rossi's Fiat Yamaha teammate Jorge Lorenzo finished third after almost falling off his bike on the opening lap, having already sealed second spot in the championship due to Stoner's non-start. He ended up 45 points behind Rossi.
Stoner, the 2007 world champion, ended in fourth place overall despite missing three races due to a mystery illness, while veteran American Colin Edwards was next after edging out young Italian Andrea Dovizioso with fourth in the Spanish race.
"Obviously this is a frustrating and disappointing way to finish the season," Stoner told the MotoGP Web site, blaming a tire temperature problem for his premature demise.
"There have been plenty of highs and lows throughout the year and we have ended on a low, but with another lesson learnt for next season. We have had this strategy for two years and not had a problem until today so I guess it is better it happened here than in the first race of next season in Qatar!
"The important thing is that after back-to-back wins in Australia and Malaysia we have shown our pace here at Valencia, and we know we have everything in place to be competitive next season if we do the job right over the winter.
"Now I am looking forward to working on the bike over the next three days and then spending a couple of months building up my physical fitness, which I haven't been able to dedicate myself 100 percent to for such a long time."
Stoner's Ducati Marlboro teammate Nicky Hayden, the 2006 world champion, edged out Toni Elias for fifth on the day for 13th overall.