Having seen his 2013 world championship hopes effectively ended by his incident with Honda team-mate Marc Marquez in the last race at Aragon, Pedrosa began the Malaysian weekend with a point to prove.
Already fastest in morning practice, his 2m00.554s lap near the end of the second session was close to record pace.
It put Pedrosa 0.553 seconds ahead of Marquez, who had previously gone half a second clear of the pack halfway through the session.
A late lap from Tech 3 Yamaha's Cal Crutchlow got the Briton up to third, ahead of works stablemate Valentino Rossi, whose title-chasing team-mate Jorge Lorenzo was only sixth.
The factory Yamahas were split by Gresini Honda rider Alvaro Bautista. The Spaniard had been quickest of all for the first 20 minutes before being deposed by Marquez, and later crashed at Turn 4.
Nicky Hayden was the only other man to have an incident, sliding into the gravel at the final corner but managing to make it back to the Ducati pits. He ended up seventh.
Aleix Espargaro led the CRT field in 11th place, with both Pramac Ducatis trailing him.