Six seconds behind Hayden, Melandri's team-mate Toni Elias
claimed a confidence boosting sixth after holding off the second factory Honda of Dani Pedrosa
- who qualified poorly then ran wide onto the dirt during lap one - while Americans Colin Edwards
and Kenny Roberts
rode to eighth and ninth placed finishes.
Konica Minolta Honda's Makoto Tamada, riding in what could be his last Japanese Grand Prix, finished as the top home rider, in tenth, after Nakano's fall - with Suzuki wild-card Kousuke Akiyoshi thirteenth on his MotoGP debut.
The lead GSV-R was that of Chris Vermeulen, who just held off team-mate John Hopkins
for eleventh despite Hopper running off track and dropping to the back of the field on lap three after tangling with Pedrosa. Casey Stoner
fell from the top ten on 'unlucky' lap 13, while Kawasaki's Randy de Puniet
also left his machine in the deep Motegi gravel.