Championship leader Jorge Lorenzo's Yamaha was second fastest, while Pedrosa's team-mate Casey Stoner crashed heavily during a rain shower, but escaped serious injury and was able to rejoin later.
Riders had only got a handful of laps in before the shower, which was brief but intense. Stoner came upon the suddenly wet track at the fast left-hander leading into the final chicane and had a violent high-side, from which he was able to walk away in some discomfort.
Going into the final quarter of an hour, Valentino Rossi (Ducati) was first to prove that slicks were viable, and soon the entire field was out on dry-weather rubber.
Pedrosa was able to beat Lorenzo's early 1m35.5s benchmark with a 1m34.587s, and then improved to a 1m34.522s, 0.161 seconds better than the best his Yamaha rival could manage in the late flurry of quick times.
Alvaro Bautista put his Gresini Honda third, ahead of the Tech 3 Yamahas of Cal Crutchlow and Andrea Dovizioso.
Stoner got back out for a handful of laps at the end of the session and managed to get up to sixth place.