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.