The Yamaha rider, the world champion in 2010, had been second best to the Australian Honda star in Thursday's session and Friday's first stretch, but then clocked a lightning 1min 55.302sec lap, just outside Stoner's 2008 circuit record.
Britain's Cal Crutchlow, on another Yamaha, was second quickest, 0.154sec behind with Stoner relegated to third spot, 0.372sec off Lorenzo's pace.
Friday's final practice also saw America's Ben Spies, on a factory Yamaha, fall off his machine and unable to improve on his 11th place.
In tricky, blustery conditions, Spain's Dani Pedrosa, on another Honda, had also come to grief in the first session although he was able to record the fifth best time later in the evening behind Andrea Dovizioso on a Yamaha in fifth.
The best Ducati performance was a sixth place by Hector Barbera riding for the Pramac satellite team with the Spaniard putting factory riders Nicky Hayden and seven-time MotoGP champion Valentino Rossi in the shade.
They were seventh and eighth respectively.
In the first session Friday, Stoner had been 0.214sec faster than Lorenzo and 0.688sec quicker than Dovizioso.
Stoner, who has won four times in the elite class in six visits to the Losail circuit, was unruffled by the strong winds as he clocked 1min 55.960, the only rider under the 1min 56sec mark in the opening period.
3rd practice times
1. Jorge Lorenzo (ESP/Yamaha) 1:55.302m 2. Cal Crutchlow (GBR/Yamaha) at 0.154, 3. Casey Stoner (AUS/Honda) 0.372, 4. Andrea Dovizioso (ITA/Yamaha) 0.603, 5. Dani Pedrosa (ESP/Honda) 0.812, 6. Hector Barbera (ESP/Ducati) 0.861, 7. Nicky Hayden (USA/Ducati) 1.100, 8. Valentino Rossi (ITA/Ducati) 1.233, 9. Stefan Bradl (GER/Honda) 1.449, 10. Alvaro Bautista (ESP/Honda) 1.469
11. Ben Spies (USA/Yamaha) 1.728, 12. Karel Abraham (CZE/Ducati) 1.921, 13. Randy de Puniet (FRA/Aprilia) 2.959, 14. Colin Edwards (USA/Suter-BMW) 3.008, 15. Michele Pirro (ITA/FTR-Honda) 3.498
1. Thomas Luthi (SUI/Suter) 2:00.479, 2. Pol Espargaro (ESP/Kalex) 0.040, 3. Esteve Rabat (ESP/Kalex) 0.639, 4. Scott Redding (GBR/Kalex) 0.751, 5. Claudio Corti (ITA/Kalex)
1. Sandro Cortese (GER/KTM) 2:08.342, 2. Romano Fenati (ITA/FTR-Honda) at 0.034, 3. Luis Salom (ESP/Kalex KTM) 0.101, 4. Maverick Vinales (ESP/FTR Honda) 0.135, 5. Miguel Oliveira (POR/Honda) 0.562