With track temperatures soaring up to 62 degrees Celsius early in the 60-minute session, a majority of the field sat out the middle section before donning the faster medium-compound tires in the final minutes to set timed laps.
Rosberg was quickest on the hard tires as well but managed to coax his Mercedes around the 5.543 km Sepang International Circuit in one minute, 39.690 seconds in the closing stages to set the fastest time of the weekend.
Hamilton complained over the radio that "his braking was all over the place" after locking up twice on slow corners early in the session but the world champion appeared more comfortable on his return to the track as he crossed the line in 1:39.874.
The Mercedes duo were the only cars to break the 1:40 seconds barrier but Ferrari continued to display plenty of pace as Kimi Raikkonen and Sebastian Vettel were comfortably the best of the rest around half a second behind Rosberg.
The Mercedes-powered Williams were also consistent and will be hoping to get among the Ferraris in qualifying and during the race as Felipe Massa edged out team mate Valterri Bottas to finish fifth in the session, the pair lapping around two-tenths slower than the Italian outfit.
McLaren's Fernando Alonso managed to rack up plenty of laps on his return to racing after the Spaniard missed the season-opener in Australia due to concussion but his best efforts were only good enough to clock the 15th-fastest time of 1:41.991.
Team mate Jenson Button was down in 18th place, ahead of the reborn Manor Marussia pair driving modified 2014 cars, but McLaren do look capable of mixing it with the Force Indias this weekend, a team they were well behind in Australia.
Qualifying is due to start at 5.00 a.m. ET.
(Editing by Sudipto Ganguly)
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