The Spaniard, refreshed from the mini summer break having suffered a sequence of injury issues, moved to the top of the times halfway through the 45-minute session.
The Honda rider then emphasised his pace with a sub-lap record of a minute 56.328 seconds on his penultimate lap.
Championship leader Casey Stoner was second quickest - 0.966s behind his team-mate.
Marco Simoncelli was third quickest on the Gresini-run factory Honda, having set the pace early in the session. But his programme was not without drama as he lost the front on the left-hander before the pits and fell. Neither rider nor bike was particularly damaged in the crash.
World champion Jorge Lorenzo, sporting a Top Gun 'Maverick' crash helmet, was fourth fastest on the Yamaha, ahead of Andrea Dovizioso on the final of the factory Hondas.
Ben Spies was sixth fastest on the second Yamaha, ahead of an impressive Jon Hopkins on the wildcard Suzuki. The American, on his second outing for the factory squad this season just outpaced team regular Alvaro Bautista, though both were two seconds off Pedrosa's pace.
Cal Crutchlow, on a circuit he knows, was ninth fastest on the Tech 3 Yamaha, just ahead of team-mate Colin Edwards.
Factory Ducati riders Valentino Rossi and Nicky Hayden were 11th and 14th.