Stoner clocked 1min 55.007sec to see off the Yamahas of world champion Valentino Rossi and Jorge Lorenzo in Saturday's session while Randy de Puniet, on a Honda, was fourth fastest.
Rossi set a time of 1:55.362 as he ensured his world title defence will begin from the front row of the grid in Losail.
His Fiat Yamaha team-mate Lorenzo, who suffered a hand injury in pre-season, put in a strong performance with the Spaniard just over half a second off Stoner’s pace.
De Puniet heads the second row after a best time of 1:55.831.
Loris Capirossi, on a Suzuki, will start a record-breaking 300th Grand Prix from fifth place.
The veteran, with a time of 1:55.899, was ahead of fellow Italian Andrea Dovizioso on a Honda.
Starting grid for Qatar Grand Prix:
MotoGP:
1. Casey Stoner (AUS/Ducati) 1:55:007
2. Valentino Rossi (ITA/Yamaha) at 0.355
3. Jorge Lorenzo (ESP/Yamaha) 0.513
4. Randy de Puniet (FRA/Honda) 0.824
5. Loris Capirossi (ITA/Suzuki) 0.892
6. Andrea Dovizioso (ITA/Honda) 0.956
7. Dani Pedrosa (ITA/Honda) 0.983
8. Colin Edwards (USA/Yamaha) 0.998
9. Nicky Hayden (USA/Ducati) 1.156
10. Hiroshi Aoyama (JPN/Honda) 1.220
125cc:
1. Marc Marquez (ESP/Derbi) 2:06.651
2. Pol Espargaro (ESP/Derbi) at 0.459
3. Nicolas Terol (ESP/Aprilia) 0.485
4. Efren Vasquez (ESP/Derbi) 0.492
5. Randy Krummenacher (SUI/Aprilia) 1.119