Sebastian Vettel, Red Bull's three-time defending world champion, was third quickest in the 90-minute warm-up drive, with his rival Fernando Alonso of Ferrari fourth.
Nico Rosberg, Adrian Sutil, Felipe Massa, Paul di Resta, Lewis Hamilton and Romain Grosjean rounded out the top 10 in the largely experimental session as teams size up their best options for Sunday's race.
Tropical heat and sudden downpours make the Malaysian Grand Prix one of the most demanding of the season with an extra challenge this year in preserving Pirelli's new, faster-degrading tyres.
The drivers will head out for another practice session at 2:00 pm (0600 GMT) with a third run-out on Saturday, followed by qualifying. The race is on Sunday.