Anglo-American Hopkins brought the second GSV-R home in sixth position, just one second ahead of Kawasaki's Randy de Puniet, while Alex Barros took seventh ahead of Pedrosa - who, against expectation, seemed to lap slower as the track dried.
Caught out by the conditions were Pedrosa's Repsol Honda team-mate and reigning world champion Nicky Hayden, who fell from sixth early on, and wet weather demon Anthony West - who saw his hopes of a dream Kawasaki debut end when he ran off track while up to fifth, from 17th on the grid, on lap 8.
A fuming West rejoined to finish 11th, while Stoner's team-mate Loris Capirossi failed to reach the flag after a determined charge saw the Italian fall from fifth when he lost the front of his GP7 into turn one with just six laps to go.
Round nine of the MotoGP World Championship, the Dutch TT at Assen, takes place next Saturday - can Stoner be stopped?
British Grand Prix:
6. de Puniet