Trulli's time of one minute 32.832 seconds on a bright and clear day at Sepang was the fastest of the weekend so far.
Austrian Christian Klien was second quickest for Red Bull in 1:32.870 while Spaniard Fernando Alonso, fastest in the morning's first 45 minute session, was third in 1:32.880 as drivers honed their setups before qualifying.
The second practice was interrupted briefly when Italy's Fisichella, winner of the Australian season-opener on March 6, lost control and spun violently across the kerb and into the gravel at turn 12 with 28 minutes remaining.
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Briton Anthony Davidson, replacing Takuma Sato at BAR after the Japanese came down with a fever, clocked the 10th best time of the final session.
Team mate Jenson Button, who has a new engine for Sunday's race after retiring strategically in Melbourne, missed the entire second practice with an oil leak.
The team said his engine was undamaged.
Ferrari's seven times world champion Michael Schumacher, chasing his first points of the season after a collision with compatriot Nick Heidfeld in Melbourne, was second fastest in the first session and 14th in the second.
