Ivan Silva, riding one of the new-for-2012 CRT machines for the Avintia Inmotec team, topped the times in Friday's first session as all the top runners chose to sit out the action on the treacherous track surface.
Silva made the most of having the best conditions to record a time of one 48.674 seconds, and with conditions not improving before the afternoon run no-one was able to beat his team.
But the second session provided the more meaningful action as the factory Hondas, Yamahas and Ducatis all took to the track.
Rossi, who endured a miserable opening race in Qatar, raised Ducati's spirits as his early lap kept him top of the timesheets for most of the session, but Repsol Honda rider Pedrosa lowered his mark by six tenths of a second late on with a lap of one minute 50.780 seconds.
Championship leader Jorge Lorenzo was up next on his Yamaha to leave two Spaniards in the top three.
World champion Casey Stoner was fourth on the second Honda while Nicky Hayden completed a good day for Ducati with fifth.
Britain's Cal Crutchlow was not able to match his excellent Qatar form in the tricky conditions as he finished eighth fastest, behind team-mate Andrea Dovizioso and the Gresini Honda of Alvaro Bautista.
Ben Spies and Stefan Bradl rounded out the top 10 while Randy de Puniet was the fastest CRT rider in 11th on his Aspar Aprilia.
Colin Edwards was 15th on his Forward Suter, ahead of Silva.
Tech 3 Yamaha rider Crutchlow said: "If we get more of the same conditions for the rest of the weekend then we have a lot of work to do.
"To be honest we struggled a little bit with a lack of rear grip and that is where we are going to have to work on because we could be racing in similar conditions on Sunday.
"This track dries really fast and with the rain tyres we are having a lot of spinning.
"Although we've got some issues with the rear grip, I am really happy with my position on the timesheets considering the problems and that makes me really confident that if we make the setting better I will be very competitive."