The Englishman was himself some way ahead of the Williams of Kazuki Nakajima, with Jarno Trulli's Toyota taking the final points position.
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Also knocked out in the opening drives were Giancarlo Fisichella and Adrian Sutil of Force India, Honda's Rubens Barrichello and Williams's Japanese driver Kazuki Nakajima.
Williams put in another solid practice performance as Nico Rosberg recorded the third fastest time with team-mate Kazuki Nakajima fifth quickest in the second practice session.
Nick Heidfeld was seventh for a resurgent BMW Sauber, with Ferrari's Kimi Raikkonen eighth, followed by the Williams of Kazuki Nakajima and Toro Rosso's Sebastien Buemi.
It was also a disappointing qualifying session for Williams, although Kazuki Nakajima will be pleased to out-qualify team-mate Nico Rosberg for the first time this season.
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Kazuki Nakajima was ninth in the second Williams, while two-time world champion Fernando Alonso was 10th ahead of his second-to-last race for Renault before replacing Raikkonen at Ferrari.
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Robert Kubica, Sebastian Vettel, Barrichello, Heikki Kovalainen and Mark Webber were involved in serious collisions with each other, while the likes of Kazuki Nakajima and Kimi Raikkonen spun into the wall.
Williams, who had high hopes for Malaysia after Nico Rosberg finished third in Melbourne, suffered when he collided with Toyota's Timo Glock and Kazuki Nakajima punctured a tire.
Kazuki Nakajima's Williams was the final finisher in seventh.
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The final pre-season testing in Jerez, Spain last week proved that the Woking-based team are heading in the right direction as Heikki Kovalainen improved to within half a second of Williams' Kazuki Nakajima, who set a fastest time of one minute 17.494.
Red Bull look tremendous through the first two sectors but struggle in the third, Brawn GP pretty much the opposite, Ferrari - and Felipe Massa in particular - effectively 'own' this track, McLaren continue to throw in the odd glimpse of decent pace and, on top of all that, Williams pair Nico Rosberg and Kazuki Nakajmia sit third and fourth right now.
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