Edwards finished fourth on Sunday, but it was only when Spies overtook Dovizioso for seventh place with six laps to go that Edwards was able to take fifth position in the standings - as the top satellite rider - by a single point.
Spies was making his Yamaha MotoGP race debut on Sunday and concluded a very impressive weekend with a strong ride, having dropped back from eighth on the grid (after Stoner's exit) to outside the top ten before fighting his way forwards again.
The result was the newly crowned World Superbike champion's best in a dry MotoGP race, having been eighth in last year's US GP for Rizla Suzuki. Few doubt that it will take long for Spies to beat his overall best MotoGP result of sixth (in the wet at Indianapolis 2008) during his first full season in 2010.
Nicky Hayden did his best to repair Ducati honour after Stoner's departure with fifth place, two-seconds behind countryman Edwards.
After his early race heroics, Elias finished his final race for Gresini Honda with a competitive sixth position and in doing so won the close six-rider fight for seventh place in the world championship.
Elias, who began the race tenth in the standings, took seventh by four points from team-mate Alex de Angelis - who finished tenth in his final Gresini ride.
Loris Capirossi came into the event joint seventh with Marco Melandri, but both Italians lost ground on Sunday. Capirossi finished a forgettable 14th while Melandri ran off track on his way to 17th during the final MotoGP appearance for the Kawasaki ZX-RR.
James Toseland concluded a two-year MotoGP career with twelfth place on the second Tech 3 Yamaha, while fellow 2010 World Superbike rider Chris Vermeulen took the final point for 15th.
Capirossi and Rizla Suzuki team-mate Vermeulen were over one minute behind Pedrosa at the flag and the GSV-R finished the season as the only motorcycle not to take a podium finish.
A test session will be held at Valencia over the next few days, when riders and teams will start work for the 2010 season.
Valencian Grand Prix:
10. de Angelis
11. de Puniet