Former superbikers James Toseland, Chris Vermeulen (Suzuki), and Nicky Hayden (Honda) fought a tremendous battle over the closing laps for sixth place.
Toseland led the trio home with Vermeulen just a couple bike lengths behind in seventh with Hayden eighth, the three riders covered by just 0.8 seconds.
Rossi was in superb overtaking form and he needed to be from ninth on grid although he realized early that he was racing for second with Pedrosa's pace.
"I had a lot of fun toady with some good overtaking and I had a great, great battle with Casey," Rossi said. "Pedrosa was incredibly strong today and I think it's impossible to say whether I could have been with him even from the from the front."
Polesitter Stoner said his bid for a repeat win in this race ended on lap one with a mysterious lack of feeling from the rear-end of his Ducati GP8.
"My set-up was great in practice and we didn't change a thing but in the race I had no feeling at the rear and it was trying come around and highside me on the brakes," Stoner said.
Fourth-place finisher Dovizioso said, "Dani was very fast today but I made a very good to be second and then I was able to keep that same pace as Rossi and Stoner, this is a great result for me."
Edwards overcame some late race problems to hold fifth.
"Dovizioso
seemed to have little more grip than me and he was able to pull away every lap," Edwards said. "I was throwing the bike in on the brakes but it would be sideways and I had to change my style."
Toseland lost early ground when forced a little wide by a Rossi braking move but finished strongly ahead of a hard-riding Vermeulen.
"I lost time early when De Angelis hit me and then over the final laps I was right with Toseland until the end," Vermeulen said. "I had more overall pace than him but I couldn't get passed."
Hayden went from third to sixth on lap one and never recovered because of fading rear grip.
"I don't think it's a tire problem, it's something in our set-up that hurts the tire life," Hayden said. "The rear brake also went towards the end and that didn't help but eighth place isn't what I wanted."
Kawasaki rider John Hopkins rode a lonely and painful race to finish tenth despite severe back bruising suffered in Friday practice.
"I'm in a lot of pain right now with my injury and that was a really tough race," Hopkins said. "It was a matter of finding a way to ride without moving around too much and although tenth isn't where I want to be it I'm pleased I achieved that today."
Suzuki rider Loris Capirossi suffered a fractured right hand when he was hit by Alex de Angelis and crashed on lap eleven.
