As was the case on Friday a wet circuit meant few riders opted to run long stints and, with track conditions not improving after the halfway mark, there was little in the way of late improvements.
That meant that Pedrosa's benchmark of one minute 50.121 seconds, set with 26 minutes remaining, was never beaten, earning the Spaniard the top spot for a second straight session.
The rest of the lead order also set their best times in the opening 30 minutes.
Yamaha's Jorge Lorenzo finished second, just over one tenth down on Pedrosa, while the second works Honda of reigning champion Casey Stoner was third.
The works Ducatis of Nicky Hayden and Valentino Rossi were then fourth and sixth respectively, split by Cal Crutchlow's Tech 3 Yamaha.
The Briton's team-mate Andrea Dovizioso finished seventh fastest ahead of LCR Honda's Stefan Bradl, Karel Abraham on the Pramac Ducati and the top CRT rider, Aspar's Randy de Puniet.
Ben Spies on the second works Yamaha finished 11th fastest.
Gresini's Alvaro Bautista was one of the few casualties of the conditions, dropping his Honda at Turn 1 in the closing stages of the session.