What should have been third practice was stretched from the usual 45 minutes to 75 minutes, with an earlier start, to make up for some of the time lost when major electricity issues at the track forced the cancellation of yesterday's afternoon session.
Stoner wasted no time when practice got back underway, throwing in a 1m49.485s - a tenth below the lap record - early on.
Honda's championship leader then improved to a 1m49.272s, putting him a second clear of the field, just as he had been for much of Friday morning, and he continued to lap consistently in the 1m49s.
It took a long time before anyone managed to erode Stoner's advantage, with his team-mate Dani Pedrosa chipping away and eventually getting the gap down to just 0.062s with his final lap.
For much of the morning the four works-specification Hondas had filled the top four, but Randy de Puniet showed eye-opening pace again on the Pramac Ducati to take third in the end. Although he had been following Andrea Dovizioso's Honda at the time, de Puniet's 1m50.003s could still not be entirely dismissed.
Dovizioso was fourth at the finish, ahead of Gresini Honda's Marco Simoncelli.
It was a tough morning for Yamaha. Ben Spies recovered from a crash at Turn 2 to take sixth on his second bike, but Jorge Lorenzo was only eighth, behind Suzuki's Alvaro Bautista - who made big strides from his Friday form.
The Ducatis of Valentino Rossi and Nicky Hayden completed the top 10.