The Honda rider again shrugged off the ankle injury that has limited his recent form and produced a string of ever-faster laps at the head of the field.
Stoner eventually reached a 1m29.665s, putting him a second clear of nearest rival Jorge Lorenzo.
With Stoner looking utterly out of reach even before qualifying, Lorenzo's focus will be on championship rival Dani Pedrosa.
In practice three at least, the Yamaha man was able to beat his Honda adversary by three tenths of a second as they lined up second and third.
The Tech 3 Yamaha duo completed the top five. Cal Crutchlow was ahead of Andrea Dovizioso, who had a minor fall.
Alvaro Bautista shrugged off a messy brush with a seagull to go sixth quickest.
Randy de Puniet took Aspar's CRT Aprilia to a giantkilling seventh. Stefan Bradl, Valentino Rossi and Karel Abraham were next up.
The session's other incident was a crash for Hector Barbera. The Pramac rider was 13th at the finish.
Local rider Kris McLaren, standing in for the injured Yonny Hernandez at Avintia, looks like he will be hard-pressed to qualify as he lapped 6.5s off the pace and 1.8s down on team-mate Ivan Silva.