As had been the case in both Friday sessions top spot was effectively the exclusive domain of Pedrosa and his title rival Jorge Lorenzo, with the latter leading early on.
With 20 minutes to run however Pedrosa shaved more than three tenths of a second off his own best to drop down to a 1m45.792s.
Lorenzo's response never materialised, the Yamaha man finishing just over two tenths of a second down.
His works team-mate Ben Spies was third, less than a tenth of a second down the road.
Andrea Dovizioso made it three Yamahas in the top four, although Gresini's Alvaro Bautista was able to split the Italian and his Tech 3 stable-mate Cal Crutchlow.
Casey Stoner, hampered by his injuries yesterday, came home seventh, within seven tenths of team-mate Pedrosa.
Valentino Rossi meanwhile was the last man to finish within one second of the ultimate pace.
Ducati team-mate Nicky Hayden was 10th, behind LCR Honda's Stefan Bradl.
An impressive late rally carried CRT rider Aleix Espargaro (Aspar) up to 11th, ahead of Pramac Ducati satellite rider Hector Barbera and Yamaha wildcard entrant Katsuyuki Nakasuga.
- Jorge Lorenzo