The fight for top spot came down to the two Honda riders, with the lead changing hands several times over the session before Pedrosa eventually sealed the issue with a 1m37.325s.
For a long while no-one else was able to join Honda in dipping under the 1m38s mark, but with 12 minutes to run Jorge Lorenzo got in on the act to go third fastest, just over three tenths down on Pedrosa.
Tech 3 Yamaha duo Cal Crutchlow and Andrea Dovizioso were next up in fourth and fifth. Dovizioso had led the inter-team battle in the early stages, but was demoted to fifth by Crutchlow with 18 minutes to run.
Late improvements sent Ducati's Valentino Rossi and then Gresini Honda's Alvaro Bautista into sixth.
Rossi had elected to run the harder compound tyre for much of the session - in contrast to the majority of the field - and ran around 10th as a consequence.
He jumped up to sixth in the final minute however, although Bautista, who was still on circuit, managed to then push the Italian down to seventh.
The second works Yamahas and Ducatis of Ben Spies and Nicky Hayden beat LCR Honda's Stefan Bradl to eighth and ninth.
Randy de Puniet once again finished top of the CRT pile. For a long time he was faster than the satellite bikes of Hector Barbera and Karel Abraham, although Barbera was able to find late improvements to move ahead of the Frenchman and into 11th.