"All week I was only thinking about the race and I really wanted to win," he said.
"In practice we struggled a lot so the team did a great job - with Casey out of the race it was more easy but we did a great race so thanks to everybody."
With Stoner out of contention from the start, Rossi and Lorenzo disputed the lead in the early stages until Lorenzo suffered a bizarre bit of bad luck.
MotoGP podium press conference
He retained control of the bike after a severe wobble, but the movement set off the airbag in his suit, taking a whole lap to go down again, and costing him vital time.
"It was a difficult race - I never felt great at this track, and then my airbag stayed open for one lap. I was not comfortable and Valentino overtook me," he said.
"It was difficult to catch him - I started to, but it was not enough to overtake him."
Britain's James Toseland finished 12th in his last race in MotoGP for the Yamaha Tech 3 team before returning to World Superbikes, and said he was leaving the competition with his head held high.
"I'm really pleased for the team, they've done a great job for me in last two years," he told BBC Sport.
"It has been a tough year, but it's been an honour to represent my country in the elite class of motorcycling.
Toseland says goodbye to MotoGP
"There has been no lack of effort and I don't feel I have failed because I put everything into it."
Britain's Bradley Smith was just edged out by new world champion Julian Simon in the 125cc race, but the biggest drama of the day came in the final ever race in the 250cc category, which will be replaced by the new Moto2 class next season.
Japan's Hiroshi Aoyama came into the race only needing to finish 11th or higher to claim the world title, but he went off track on lap nine, returning to the race in 11th place.
Italy's Marco Simoncelli, who was the only person who could beat Aoyama to the title, was leading when he crashed out with seven laps left, allowing Spaniard Hector Barbera to win the race and take second place in the championship from Simoncelli.
Valencia MotoGP race result:
1 D Pedrosa (Spn) Honda 46'47.553 2 V Rossi (Ita) Fiat Yamaha 46'50.183 3 J Lorenzo (Spn) Fiat Yamaha 46'50.466 4 C Edwards (US) Tech 3 Yamaha 47'20.068 5 N Hayden (US) Ducati 47'22.138 6 T Elias (Spn) Honda 47'22.441 7 B Spies (US) Yamaha 47'25.259 8 A Dovizioso (It) Honda 47'25.917 9 M Kallio (Fin) Ducati 47'30.044 10 A de Angelis (SM) Honda 47'31.242 11 R de Puniet (Fr) Honda 47'33.571 12 J Toseland (GB) Tech 3 Yamaha 47'37.779 13 A Espargaro (Sp) Pramac 47'44.721 14 L Capirossi (Ita) Suzuki 47'54.430 15 C Vermeulen (Aus) Suzuki 47'59.254 16 G Talmacsi (Hng) Honda 48'01.958 17 M Melandri (It) Kawasaki 48'20.978
2009 MotoGP championship final placings:
1 V Rossi (Ita) Fiat Yamaha 306 2 J Lorenzo (Sp) Fiat Yamaha 261 3 D Pedrosa (Sp) Repsol Honda 234 4 C Stoner (Aus) Ducati 220 5 C Edwards (USA) Tech 3 Yamaha 161 6 A Dovizioso (Ita) Repsol Honda Team 160 7 T Elias (Spn) San Carlo Honda Gresini 115 8 A de Angelis (SM) San Carlo Honda Gresini 111 9 L Capriossi (Ita) Rizla Suzuki 110 10 M Melandri (Ita) Hayate Racing Team 108 11 R de Puniet (Fr) LCR Honda MotoGP 106 12 C Vermeulen (Aus) Rizla Suzuki MotoGP 106 13 N Hayden (USA) Ducati 104 14 J Toseland (GB) Tech 3 Yamaha 92 15 M Kallio (Fin) Pramac Racing 71 16 N Canepa (Ita) Pramac Racing 38 17 G Talmacsci (Hng) Scot Racing Team MotoGP 19 18 A Espargaro (Spn) Pramac Racing 16 19 S Gibernau (Spn) Grupo Francisco Hernando 12 20 B Spies (USA) Yamaha Team 9 21 Y Takahashi (Jpn) Scot Racing Team MotoGP 9
250cc race result:
1 H Barbera (Spn) Aprilia 44mins 10.601secs 2 A Bautista (Spn) Aprilia 44:14.264 3 R De Rosa (Ita) Honda 44:16.266
250cc championship final placings:
1 H Aoyama (Japan) Honda 261 pts 2 H Barbera (Spain) Aprilia 239 3 M Simoncelli (Italy) Gilera 231
125cc race result:
1 J Simon (Spn) Aprilia 41mins 17.553secs 2 B Smith (GB) Aprilia 41:17.773 3 P Espargaro (Spn) Derbi 41:29.676
125cc championship final placings:
1 J Simon (Spn) Aprilia 289 pts 2 B Smith (GB) Aprilia 223.5 3 N Terol (Spn) Aprilia 179.5
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