The Lotus driver, world champion in 2007 and a surprise but emphatic winner at last week's season-opening Australian Grand Prix, dodged a heavy shower to clock the day's fastest time of 1min 36.569sec in the second session.
Red Bull's Sebastian Vettel, on the hunt for his fourth straight world title, was just two-hundredths of a second slower at the tropical Sepang circuit while Felipe Massa and Fernando Alonso were third and fourth for Ferrari.
Red Bull pilot Mark Webber, who led the opening 90-minute session, timed fifth in the second stanza while Lotus' Romain Grosjean, despite a bumpy excursion across the trackside grass, was sixth.
Nico Rosberg, Paul di Resta, Lewis Hamilton and Adrian Sutil were the remaining top 10 drivers after a difficult session which was punctuated by a track-clearing deluge midway through.
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 Formula One supplier Pirelli's new, faster-degrading tyres.
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