Toyota's Brazilian Ricardo Zonta, one of four drivers allowed to run on Fridays only, lapped the Sepang circuit in one minute 34.092 seconds.
McLaren's Spanish test driver Pedro de la Rosa was second quickest, with a time of 1:35.144, ahead of Red Bull's Italian reserve Vitantonio Liuzzi.
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With engines now having to last for two successive races, and Malaysia's hot and humid conditions being a real test of man and machine, others limited their mileage as track temperatures hovered around 50 degrees Celsius.
Renault's Italian Giancarlo Fisichella, winner in Melbourne, and his Spanish team mate Fernando Alonso did not set a time with both venturing out for just two installation laps in the searing heat.
McLaren's Kimi Raikkonen, winner at Sepang in 2003, and Colombian Juan Pablo Montoya did six and five laps respectively in the one-hour session and were seventh and eighth quickest.
BAR's strategy of retiring their cars in Melbourne to enable Briton Jenson Button and Japan's Takuma Sato to change engines without penalty appeared to be paying off with Button fifth fastest.
Germany's Nick Heidfeld, who also has a new BMW engine in his Williams after retiring in Australia following his collision with Schumacher, was sixth.
Canada's Jacques Villeneuve, the 1997 champion whose Formula One future has been called into question after being one of the slowest drivers in the season-opener, again trailed his Brazilian team mate Felipe Massa.
Villeneuve lapped in 1:38.416 while Massa clocked 1:36.963.
There was little incident in the session, other than Indian Narain Karthikeyan spinning harmlessly into the gravel and Sato also spinning off before rejoining.
