World champion Jorge Lorenzo, as well as Repsol Honda duo Dani Pedrosa and Casey Stoner, sat out the later session as Randy De Puniet topped the timesheets.
With Lorenzo's Yamaha, as well as Pedrosa and Stoner, missing from the fastest times it was left to the San Carlo Honda of Michele Pirro to take second place with Nicky Hayden third for Ducati.
The morning practice session was also weather-affected with Hayden setting the pace.
Pedrosa was second with home favourite Lorenzo in third and Stoner, participating in his final MotoGP race ahead of his retirement, down in 10th.
The third practice session is due to take place in much better weather conditions tomorrow [Saturday] morning with the teams unable to take much technical data from today's [Friday] washout.
Lorenzo sealed his second title last time out in Australia and has already made it clear he wants to wrap the season up in style with a win in his home race.