Top spot had belonged exclusively to Honda during the 40 minute session, Pedrosa and team-mate Casey Stoner trading times throughout, although Yamaha's Jorge Lorenzo was able to shadow the duo and stay within two tenths of a second.
It was Stoner who had looked most likely to end the session on top, having got down to a 1m22.444s as the chequered flag fell.
Pedrosa's final effort carried the Spaniard to the top of the timesheets however, at a circuit where he was victorious in both 2011 and 2010.
The top three riders' pace proved too much for the rest of the field, although Andrea Dovizioso was able to drop below the 1m23s mark in the late stages. He ended fourth fastest as a result, just over half a second adrift.
Tech 3 Yamaha stablemate Cal Crutchlow, still riding with a fractured ankle, ended the session in fifth, less than two tenths down on Dovizioso.
Hector Barbera finished as the fastest Ducati, putting his satellite Pramac machine sixth ahead of works rider Nicky Hayden, Gresini's Alvaro Bautista - who will start from the back of the grid following his Dutch TT clash with Lorenzo - and LCR Honda's Stefan Bradl.
The second works Yamaha of Ben Spies rounded out the top 10 ahead of Valentino Rossi on the second works Ducati.
Franco Battaini, replacing Karel Abraham at the Kardion Ducati squad, suffered one incident through the gravel 13 minutes from the end. He finished down in 18th position.
Pol Espargaro of Pons 40 HP Tuenti topped the first Moto2 session.
Espargaro, third in the championship, was followed by leader Marc Marquez of CatalunyaCaixa Repsol and Briton Bradley Smith of Tech 3.
FTR Honda’s Jakub Kornfeil went fastest in the opening Moto3 practice ahead of Kalex KTM duo Hector Faubel and Luis Salom.
Series leader Maverick Vinales, also on a FTR Honda, was sixth.