Australian Stoner was world champion in 2007
Former world champion Casey Stoner set the fastest lap time in the final MotoGP pre-season test in Qatar.
Stoner's time of one minute, 55.353 seconds beat the previous night's pace setter Valentino Rossi, who was under five hundredths of a second behind.
Jorge Lorenzo, who rode despite having not yet fully recovered from a hand injury, finished sixth in 1:56.504.
Australian Stoner fell shortly after setting the fastest time of the two floodlit tests but was not injured.
At the end of the two races, Ducati rider Stoner, 24, topped the times in first place overall.
Defending world champion Rossi, 31, was second, five places ahead of his 22-year-old Fiat Yamaha team-mate Lorenzo, who displaced his thumb and fractured his hand less than five weeks ago.
Italian Andrea Dovizioso was third overall, with rookie Ben Spies fourth and fellow American Nicky Hayden fifth.
The tests were the last for the 17 world championship riders ahead of the new MotoGP season, which gets under way on 11 April in Qatar.
Qatar testing times:
1 C Stoner (Aus) Ducati 1:55.353
2 V Rossi (Ita) Fiat Yamaha Team 1:55.402
3 A Dovizioso (Ita) Repsol Honda Team 1min 55.879
4 B Spies (USA) Monster Yamaha Tech 3 1:55.954
5 N Hayden (USA) Ducati 1:56.115
6 L Capirossi (Ita) Rizla Suzuki MotoGP 1:56.195
7 J Lorenzo (Spn) Fiat Yamaha Team 1:56.504
8 R de Puniet (Fr) LCR Honda MotoGP 1:56.504
9 C Edwards (USA) Monster Yamaha Tech 3 1:56.540
10 M Kallio (Fin) Pramac Racing 1:56.767
11 A Espargaro (Spn) Pramac Racing 1:56.897
12 A Bautista (Spn) Rizla Suzuki 1:56.898
13 D Pedrosa (Spn) Repsol Honda 1:56.935
14 M Melandri (Ita) San Carlo Honda Gresini 1:57.222
15 H Barbera (Spn) Paginas Amarillas Ducati 1:57.223
16 H Aoyama (Jpn) Interwetten Honda 1:57.251
17 M Simoncelli (Ita) San Carlo Honda Gresini 1:57.379