Few ventured out in the early stages when the track was at its wettest, but after Mattia Pasini served notice that slicks had become the best option by going fifth, times began to tumble rapidly.
Honda's Casey Stoner was the first to make his move, going almost two seconds clear at the top, but within five minutes he had been relegated to 11th as Tech 3's Andrea Dovizioso led a spate of improvements.
Eight minutes from the end Dovizioso had once again displaced Stoner at the top of the timesheets, but with the track now ostensibly dry it came down to a final shoot-out in the closing five minutes.
Dovizioso improved his own benchmark and dipped into the 1m33s, but his lead was fleeting as Stoner shaved off three hundredths of a second to go top.
With Dovizioso pulling into the pits, Stoner's main competition then came from Yamaha's Jorge Lorenzo and the second works Honda of Pedrosa.
Lorenzo ultimately fell short, the final sector his chief downfall as he ended the session fourth, just over one tenth down on Dovizioso.
Pedrosa however found a significant chunk in the final minute, his 1m33.638s enough to earn him pole by more than three tenths of a second.
Cal Crutchlow and Ben Spies finished fifth and sixth fastest to complete an all-Yamaha second row, while behind them the Ducatis of Valentino Rossi and Hector Barbera (Pramac) were split by Alvaro Bautista's Gresini Honda.
The satellite Cardion Ducati of Karel Abraham then edged out Nicky Hayden's works counterpart for 10th, while Aspar's Randy de Puniet put his CRT machine above the LCR Honda of Stefan Bradl, who suffered a high side at Museum 25 minutes into the session.