As was the case in Friday's second session, conditions were once again too wet for slicks and too dry for wets, leading to a dearth of early running.
Exacerbated by a new surface that does not lend itself to swift drying, the conditions meant that by the halfway mark just 11 riders had set a time, with Phillip Island race-winner Casey Stoner, Ducati's Valentino Rossi and Tech 3's Cal Crutchlow not going out at all.
That collective reluctance did at least dissipate over the final minutes, when the track finally dried out enough for slicks.
While there was still little the teams could learn on the slippery surface, rendering laptimes largely meaningless, there was at least cause enough for all the usual frontrunners to head out.
It was Honda rider Pedrosa who ended on top, the Spaniard eventually working his way down to a 1m33.033s.
That was six tenths faster than Tech 3 duo Andrea Dovizioso and Crutchlow, with the Italian stealing ahead of the Briton as the chequered flag fell.
LCR Honda's Stefan Bradl came home fourth, the last rider to get within one second of Pedrosa.
Nicky Hayden on the second Ducati was fifth fastest ahead of newly-crowned champion Jorge Lorenzo, Gresini's Alvaro Bautista and Aspar CRT rider Randy de Puniet.
Casey Stoner was ninth fastest, with Rossi two spots further back in 11th.