The Repsol Honda rider, who started from second on the grid, took the lead right at the start and immediately opened a gap over the rest of the field.
When the gap got up to three seconds, Pedrosa was curiously shown a pit-board on lap 12 saying his advantage was only 1.1 seconds. While the gap rose to up to four and a half seconds two thirds of the way through the race, Pedrosa ultimately won by 2.8 seconds over Fiat Yamaha's Valentino Rossi.
The Italian ran throughout the race in a pack with rookie teammate Jorge Lorenzo and the other works Honda of Nicky Hayden.
The three ultimately ended the race in that order, even though Rossi nearly gave second place away to Lorenzo when he started celebrating on the main straight one lap too early.
Andrea Dovizioso had reached fifth place in the last laps with his JiR Team Scot Honda but threw it all away on the last corner of the last lap when he went wide and was overtaken by Loris Capirossi's Rizla Suzuki, James Toseland's Tech 3 Yamaha, and John Hopkins's Kawasaki.
Honda Gresini's Shinya Nakano finished in ninth place ahead of the Suzuki of Chris Vermeulen.
It was a day to forget for reigning champion Casey Stoner. The Ducati Marlboro rider got up to third by the end of the first lap after starting in seventh place, but dropped to last place after going through the gravel on lap three.
The Australian recovered many positions but had another off while fighting for tenth place with Nakano and Vermeulen with four laps to go, and had to be content with 11th place, ahead of teammate Marco Melandri.
Colin Edwards, who qualified third with his Tech 3 Yamaha, went in the gravel from sixth place on lap five, rejoined the track, but retired in the pits one lap later.
Pos Rider Bike Time
1. Daniel Pedrosa Honda (M) 45:35.121
2. Valentino Rossi Yamaha (B) + 2.883
3. Jorge Lorenzo Yamaha (M) + 4.339
4. Nicky Hayden Honda (M) + 10.142
5. Loris Capirossi Suzuki (B) + 27.524
6. James Toseland Yamaha (M) + 27.808
7. John Hopkins Kawasaki (B) + 28.296
8. Andrea Dovizioso Honda (M) + 28.449
9. Shinya Nakano Honda (B) + 32.569
10. Chris Vermeulen Suzuki (B) + 35.091
11. Casey Stoner Ducati (B) + 42.223
12. Marco Melandri Ducati (B) + 44.498
13. Anthony West Kawasaki (B) + 45.807
14. Alex de Angelis Honda (B) + 45.871
15. Toni Elias Ducati (B) +1:09.558
16. Sylvain Guintoli Ducati (B) +1:14.442
Retirements:
Rider Bike Laps
Colin Edwards Yamaha (M) 6
Randy de Puniet Honda (M) 0
autosport.com