As was the case in the opening session the Australian was quickly into his stride, dipping into the 1m30s early on to move around one second clear of the field.
As others then improved, so did Stoner and with 12 minutes to go he set a new weekend benchmark with a 1m29.999s.
At the time no other rider had even broken the 1m31s barrier, although Dani Pedrosa on the second Honda was at least able to rectify that with a 1m30.884s three minutes from the flag.
That put him just over one tenth clear of championship rival Jorge Lorenzo, who holds a dwindled 23-point advantage over his compatriot coming into the penultimate round of 2012.
Despite struggling with bronchitis, Tech 3 Yamaha's Cal Crutchlow was next up in fourth, ahead of team-mate Andrea Dovizioso.
Honda satellite riders Alvaro Bautista (Gresini) and Stefan Bradl (LCR) rounded out the top seven ahead of works Ducati riders Valentino Rossi and Nicky Hayden.
Neither of the Desmosedici riders were able to get within two seconds of Stoner's best.
Randy de Puniet on the lead CRT ended 10th fastest, ahead of the prototype Ducatis of Hector Barbera and Karel Abraham.