Reigning champion Stoner - who had been quickest for Honda in practice one and two - led most of the Friday night session as well, but was pushed back to third in a flurry of late fast times.
Lorenzo put in a one minute 55.536 seconds on his Yamaha to depose Stoner's early 1:55.674 going into the final minutes.
The Spaniard was almost immediately beaten by Tech 3's Cal Crutchlow - who has looked rapid throughout practice - but on his next lap Lorenzo regained the top spot by 0.154 seconds over the satellite Yamaha man.
Stoner never managed to improve on his time from the early runs, and lost time behind Alvaro Bautista's Gresini Honda on his final flying lap.
Both Tech 3 Yamahas were near the front, as Andrea Dovizioso backed up Crutchlow's strong form in fourth.
But it was a bad night for the second works Yamaha rider Ben Spies, who crashed early on and was only 11th in the times, having completely few laps even after rejoining.
Dani Pedrosa was 0.812 seconds off the pace in fifth on the second factory Honda.
Pramac's Hector Barbera was again quickest Ducati, beating works riders Nicky Hayden and Valentino Rossi to sixth.
Randy de Puniet returned to the top of the unofficial CRT class, despite crashing his Aspar Aprilia late on. The Frenchman limped away from the scene.