Pedrosa was the first rider to dip below the 1m43s mark, which was enough to keep him on top for the majority of the session.
With seven minutes to go, however, Stoner captured the top spot with a two-lap salvo, shaving one tenth of a second off Pedrosa's benchmark.
Yamaha's Jorge Lorenzo moved into third in the final 30 seconds of the session, finishing just 0.233s down on Stoner.
Tech 3 Yamaha's Cal Crutchlow sealed fourth, although Ben Spies' Yamaha, LCR Honda's Stefan Bradl and the works Ducati of Nicky Hayden all finished within seven hundredths of a second of his time.
A close session was also reflected in the fact that Karel Abraham on the Cardion Ducati finished 0.540s down on Stoner in eighth, and also in the fact that Tech 3's Andrea Dovizioso, second fastest with 15 minutes to go, was bumped down to ninth at the finish.
Alvaro Bautista (Gresini Honda), Valentino Rossi (Ducati) and Hector Barbera (Pramac Ducati) rounded out the top 12, all three lapping within nine tenths of a second of Stoner.
Aspar's Randy de Puniet topped the CRT standings in 13th, while Forward's Colin Edwards, returning this weekend after injury forced him to miss Le Mans, was 17th.
Interwetten-Paddock’s Tom Luthi was quickest in the first
In the opening