The 22-year-old claimed the championship lead from Casey Stoner as the Australian struggled on his Ducati.
Pedrosa rocketed past pole sitter and arch-rival Jorge Lorenzo to take the lead on the first corner and proceeded to lay down a series of blistering laps to open up a handsome over the rest of the field.
Five-times MotoGP champion Valentino Rossi claimed second place, some three seconds behind Pedrosa, while his Yamaha team mate Lorenzo finished third.
American Nicky Hayden was fourth on his Honda but defending champion Stoner finished back in 11th place after taking two detours on the gravel early in the race.
Fellow Australian Chris Vermuelen was tenth on his Suzuki.