Sepang has been a happy hunting ground for Pedrosa in recent years and the Repsol Honda rider topped the timesheets in the first run (two minutes, 1.379 seconds), 0.014secs quicker than NGM Forward Racing's Aleix Espargaro.
A deluge of torrential rain caused the second session to be delayed and it was no surprise to see the riders lap slower in testing conditions when they were finally allowed out on the track.
Jorge Lorenzo (Movistar Yamaha) produced the best time, but was over 13 seconds slower than fellow Spaniard Pedrosa managed earlier in the day.
Nevertheless, Lorenzo was third fastest overall in the combined times ahead of world champion Marc Marquez (Repsol Honda), who is still aiming to equal Mick Doohan's premier-class record of 12 race wins in a season.
Stefan Bradl (LCR Honda) rounded off the top five, with Valentino Rossi (Movistar Yamaha), victorious at Phillip Island last time out, in sixth.