Hayden, who started on the outside of the front row, put up a determined defence, but his expected tyre endurance problems duly emerged late in the race and the American eventually slid all the way back to eighth.
Loris Capirossi pipped 2008 Rizla Suzuki team-mate Chris Vermeulen by just 0.058secs to take fifth on his Ducati farewell, while Alex Barros brought his 21-year world championship career to a close with a competitive seventh position.
Behind Hayden, Randy de Puniet's last Kawasaki ride ended in ninth, with Toni Elias completing the top ten for Honda Gresini. Elias' 2008 d'Antin Ducati team-mate Sylvain Guintoli finished his rookie MotoGP season with an eleventh position for Dunlop Tech 3 Yamaha, having qualified an excellent fifth.
Carlos Checa, riding in his 220th and last grand prix before moving to World Superbikes, finished twelfth for Honda LCR - despite being plagued by severe stomach problems all weekend, forcing several trips to the local hospital.
The final world championship point went to Guintoli's team-mate Makoto Tamada, on what looks like being his last grand prix appearance.
Chaz Davies, due to ride in his fourth MotoGP of the season, didn't start the race due to injuries sustained in practice.
9. de Puniet