Behind the top four, Colin Edwards enjoyed his best race of the season with fifth place for Monster Yamaha Tech 3, after re-passing rookie Marco Simoncelli (Gresini Honda).
Another rookie, Alvaro Bautista, was seventh for Suzuki, having inherited the position when team-mate Loris Capirossi suffered a mechanical failure while just in front of the Spaniard late in the race.
Capirossi was the only non-finisher, although Americans Ben Spies and Nicky Hayden ran off track almost simultaneously on lap two at the end of the back straight.
The incident dropped them both to the back of the 16-rider field. Future factory Yamaha rider Spies then rose back up to eighth for Tech 3 at the flag, while present factory Ducati rider Hayden reached twelfth.
The Japanese Grand Prix had originally been scheduled to take place in April, but had to be postponed due to the Icelandic volcano grounding flights from Europe.
Today's race was attended by just over 40,000 fans - a poor turnout given the huge involvement Japan has in motorcycle sport.
Japanese Grand Prix:
9. de Puniet