The enlarged 20-rider field had found the new Malaysian Grand Prix asphalt incredibly slippy during Friday morning's first free practice session - and a rain shower before the second session initially reduced grip levels even further. However, the track dried relatively quickly and began releasing ever-increasing traction.
Many riders had chosen to wait in the pits for the first part of the afternoon hour while the moisture cleared - including new world champion Casey Stoner, who had held a 0.572secs advantage over Dani Pedrosa in morning practice.
Stoner appeared 15 minutes into the second session, then took just four laps to hit the top, by over one second. Repsol Honda rider Pedrosa fought back to sit fastest at the halfway stage, before Stoner trimmed 0.053secs from the Spaniard's time heading into the last quarter.
de Puniet had been between Stoner and Pedrosa at the halfway stage, but jumped confidently clear by 0.797secs heading into the final ten minutes - and couldn't be caught. Ducati star Stoner came just 0.011secs short of the flying Frenchman on his very final lap, while Stoner's future team-mate Marco Melandri knocked Pedrosa from third, albeit 0.744secs from Randy.
Wet weather ace Anthony West, fastest in the early stages, completed a strong opening day for Team Green with fifth, while Melandri's Honda Gresini team-mate Toni Elias gave a timely reminder of his talents in sixth.
Rookie Sylvain Guintoli was a strong seventh for Dunlop Yamaha Tech 3, while Rizla Suzuki riders John Hopkins and Chris Vermeulen were line astern in eighth and ninth. After Pedrosa, team-mate Nicky Hayden was the next best Michelin rider, down in tenth.
But the other Michelin backed factory team, Fiat Yamaha, faired far worse; Colin Edwards clocking the 14th fastest time, with seven times world champion Rossi just 16th.
Wild-card Nobuatsu Aoki split the M1s on his 2008 GSV-R prototype, while Chaz Davies was 0.476secs slower than Rossi in 17th for d'Antin Ducati. Shinya Nakano fell twice on his way to 18th, while Makoto Tamada and Kurtis Roberts completed the field.
Friday practice:1. de Puniet
2. Stoner
3. Melandri
4. Pedrosa
5. West
6. Elias
7. Guintoli
8. Vermeulen
9. Hopkins
10. Hayden
11. Checa
12. Barros
13. Capirossi
14. Edwards
15. Aoki
16. Rossi
17. Davies
18. Nakano
19. Tamada
20. Roberts