Rookie of the Year Ben Spies, who replaces Rossi next season, began the race level on points with fellow American Nicky Hayden for sixth in the championship, a position that automatically went in Spies' favour after Hayden crashed out of second place early in the race.
The Ducati rider lost the front through the third-gear first turn, while Spies rode to fourth on his final appearance for Tech 3 after carving past Andrea Dovizioso and Marco Simoncelli in the closing stages.
Former title contender Pedrosa finished seventh, while Hector Barbera gave the Aspar Ducati team eighth place at the end of the team's first MotoGP season.
Fellow rookie Alvaro Bautista was ninth for Suzuki, while Randy de Puniet's 200th grand prix, and last for LCR Honda, ended with tenth position. The Frenchman will ride for Pramac Ducati next season.
Aleix Espargaro, starting his final MotoGP race before switching to Moto2 next year, signed off with eleventh in front of experienced rivals Colin Edwards (Tech 3) and Marco Melandri (Gresini).
Former MotoGP title runner-up Melandri was making his last premier-class appearance before moving to World Superbike.
Fellow Italian Loris Capirossi retired with a technical problem from his final Suzuki race, and what looks like being the last race for Suzuki as a two-rider team. Capirossi will switch to Pramac Ducati next year.
Hiroshi Aoyama gave Interwetten 14th in the team's final race, while Carlos Checa's second and final stand-in appearance for Pramac brought one world championship point for 15th and last.
A test session, when Valentino Rossi will make his Ducati debut and Casey Stoner his first factory Honda appearance, will be held at Valencia on Tuesday and Wednesday.
Valencia Grand Prix:
10. de Puniet