Hayden, who started the race third, was forced to go to a backup bike after taking a high-speed tumble during the early practice session. Casey Stoner, the 2007 world champion, was the winner in the season-ending MotoGP event.
Hayden now moves on to Ducati, where he'll join Stoner as testing gets under way for the 2009 season.
"I rode hard this weekend," Hayden said. "Now, I'm looking forward to doing something different. I have to finish off by saying thanks to my team, to Honda, to Michelin and to everybody here. They made me a world champ. I'm grateful to them all."
Dani Pedrosa, Hayden's Repsol teammate, was second. He finished third in the overall point standings.
Hayden was sixth.
-- Philpot's Hayden Gillim finished 10th in the Red Bull Rookies Cup race at Valencia after taking the pole position during qualifying on Saturday in the final event of the two-race showdown between young riders from the U.S. and riders from the rest of the world.
The world riders continued the domination they showed at the first race in September at Indianapolis Motor Speedway. Mathew Hoyle of Great Britain was first, followed by Spain's Luis Salom.
Jake Gagne finished third to lead the U.S. contingent.
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