The 45-minute session was effectively split into two, with a shower of rain just eight minutes into the session sparking a 10-minute period of silence as the riders waited for the track to dry.
Once it did, the times quickly tumbled, Stoner and Yamaha's Ben Spies spending much of the session trading fastest times. The Honda rider eventually landed the killer blow with just minutes left in the session, his 2:04.791 best beating Spies by just 0.034 seconds.
Alvaro Bautista was third fastest on the Gresini Honda, while Nicky Hayden backed up his impressive wet weather performance from free practice one to go fourth fastest in the dry.
The news was nowhere as good for his Ducati team-mate Valentino Rossi, who went from being fastest in the first session to 11th, and last of the prototypes, in the second session.
In a session with no major incidents, Stefan Bradl made the highlights reel with a very small off mid-session. It did not slow him down, the LCR Honda rider banging out a quick lap after the flag to go fifth fastest, ahead of the Tech 3 Yamaha of Andrea Dovizioso, and the factory Yamaha of Jorge Lorenzo.
Cal Crutchlow (Tech 3) was another rider to set his best time after the flag, his time putting Honda's Dani Pedrosa and Pramac Ducati's Hector Barbera at the back of the top 10.
Randy de Puniet (Aspar Aprilia) was best of the CRT machines, his fastest time some 3.1s slower than Stoner's benchmark.
Second practice results
1. Casey Stoner Honda 2m04.791s
2. Ben Spies Yamaha 2m04.825s + 0.034s
3. Alvaro Bautista Gresini Honda 2m04.995s + 0.204s
4. Nicky Hayden Ducati 2m05.353s + 0.562s
5. Stefan Bradl LCR Honda 2m05.391s + 0.600s
6. Andrea Dovizioso Tech 3 Yamaha 2m05.448s + 0.657s
7. Jorge Lorenzo Yamaha 2m05.488s + 0.697s
8. Cal Crutchlow Tech 3 Yamaha 2m05.574s + 0.783s
9. Dani Pedrosa Honda 2m05.886s + 1.095s
10. Hector Barbera Pramac Ducati 2m06.084s + 1.293s
11. Valentino Rossi Ducati 2m07.125s + 2.334s
12. Randy de Puniet Aspar Aprilia 2m07.893s + 3.102s
13. Michele Pirro Gresini FTR-Honda 2m08.535s + 3.744s
14. Mattia Pasini Speed Master Aprilia 2m08.975s + 4.184s
15. Yonny Hernandez Avintia FTR-Kawasaki 2m09.078s + 4.287s
16. Aleix Espargaro Aspar Aprilia 2m09.379s + 4.588s
17. James Ellison Paul Bird Aprilia 2m09.944s + 5.153s
18. Danilo Petrucci Ioda-Aprilia 2m11.325s + 6.534s
19. Colin Edwards Forward Suter-BMW 2m11.600s + 6.809s
20. Ivan Silva Avintia Inmotec-Kawasaki 2m12.737s + 7.946s