As was the case in yesterday's sessions tyre choice proved critical, with Pedrosa's time - a 1m41.646s, the fastest ever on a MotoGP bike at Barcelona - coming when he switched to a softer rear compound.
Pedrosa's two-lap flurry, set as the chequered flag was readied, deprived works Honda team-mate of top spot by just over three tenths of a second.
Stoner had himself produced a late burst to depose Tech 3 Yamaha's Andrea Dovizioso, who had been on top for the majority of the session after becoming the first rider to dip under the 1m42s mark.
Of the top three however, only Stoner set his time on the harder front and rear compounds.
Pramac Ducati's Hector Barbera ran toward the front for the entire session and eventually ended fourth, ahead of the works Ducati rider Nicky Hayden. The Texan followed Stoner's lead by opting for hard front and rears.
Yamaha's Jorge Lorenzo ended more than one second down on Pedrosa in sixth, ahead of Stefan Bradl (LCR Honda), Cal Crutchlow (Tech 3 Yamaha) and Valentino Rossi (Ducati).
Having complained about the set-up of his Ducati following the opening two practice sessions, Rossi opted to switch back to the carbon fibre swingarm he had used prior to the team's recent Mugello test.
Gresini Honda's Alvaro Bautista finished 10th fastest ahead of the second works Yamaha of Ben Spies.
Aspar's CRT duo Randy de Puniet and Aleix Espargaro meanwhile occupied 12th and 13th, with the Cardion Ducati of Karel Abraham 14th.