After qualifying on pole, Pedrosa was forced to race his spare bike after an 'issue' with his number one machine during a warm-up practice start saw him loop his factory Honda.
"We had an issue with the machine on my practice start in the warm-up so I was racing my second bike," said the Spaniard. "The feeling was not perfect but still I was able to push hard and fight for positions for most of the race."
Pedrosa settled into third in the early stages, was demoted to fifth by Rossi and Marco Melandri, but then regained third when team-mate Nicky Hayden retired and Melandri began suffering tyre problems.
Encouragingly, Pedrosa was able to keep in touch with fellow Michelin rider Rossi for the entire race - but both were surpassed by the Bridgestone-shod Ducati of Loris Capirossi, who finished second to team-mate Casey Stoner.
"In the last ten laps the grip from the tyres began to fall away quite quickly and I had a lot of wheelspin and the machine was sliding when I tried to open the throttle," confirmed Dani, who finished 1.6secs behind Rossi. "Casey was very fast again here and I don't think we could have stayed with him today but it's a shame not to be on the podium. We've had two pole positions in a row and haven't converted them into very good results so hopefully we can change this for the next race in Malaysia next weekend [in Sepang]."