Kubica's team-mate Nick Heidfeld and the second Toyota of Jarno Trulli completed the top 10.
BBC: Hamilton edged out Ferrari's Kimi Raikkonen by 0.102secs
The Englishman was demoted to third place behind Ferrari's Felipe Massa and BMW Sauber's Nick Heidfeld.
Russian Vitaly Petrov initially partnered Nick Heidfeld before Brazilian Bruno Senna replaced the German in August.
Heidfeld and Rosberg both drove unobtrusively excellent races to take the final two podium positions.
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But it seems to me that he also has more going for him than Pizzonia or Heidfeld.
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Removal of the two driver aids was weighing on a number of minds, including Heidfeld's team-mate Robert Kubica.
And he was third fastest overall on Saturday, behind Nick Heidfeld in the Renault and Fernando Alonso's Ferrari.
Alonso's time stood until Heidfeld beat it with a 1:20.361 lap with 80 minutes of the test remaining.
BBC: Nick Heidfeld heads Fernando Alonso at his Renault test
Ferrari's Fernando Alonso was the long-time pace-setter but Heidfeld beat him by 0.132 seconds late in the afternoon.
BBC: Nick Heidfeld heads Fernando Alonso at his Renault test
The team have replaced Pedro de la Rosa with Nick Heidfeld for the final five races of this season.
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Heidfeld has collected 34 points, three more than his Russian teammate Vitaly Petrov.
Nick Heidfeld was a fine fourth for Williams with team-mate Mark Webber sixth.
German Nick Heidfeld and Britain's Anthony Davidson, who impressed as BAR's test driver last season, are also in the running.
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Heidfeld, a veteran of 172 grands prix and a former team-mate of Kubica, wasted no time in proving his credentials.
BBC: Nick Heidfeld heads Fernando Alonso at his Renault test
Germans Nick Heidfeld of BMW Sauber and Nico Rosberg of Williams were seventh and eighth in the final points positions.
Heidfeld held a watching brief in the early laps and stayed out of trouble to benefit from Kovalainen's late problem.
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Heidfeld could choose one of the new teams and work his way up, just as he did with Jordan in 2004.
Nick Heidfeld completed a BMW one-two with Red Bull's David Coulthard third.
German Heidfeld was being evaluated by Renault as a potential stand-in for Kubica, who suffered serious injuries in a rally crash last weekend.
BBC: Nick Heidfeld heads Fernando Alonso at his Renault test
But Renault's sixth-placed Alonso followed by Sebastian Vettel and BMW Sauber's Nick Heidfeld will all be expected to push hard from the start.
Heidfeld was left to fend off Fernando Alonso's Renault, which had run fifth from the start and, like Kubica, also needed to stop again.
"Autumn in Australia brings the possibility of rain, which would make driving without traction control and engine braking control a real challenge, " Heidfeld said.
However, BMW Sauber's Nick Heidfeld was left bemused by Mosley's comments.
Heidfeld led as the safety car pulled off, ahead of eight other cars which did not stop during the caution period, and Kubica in 10th place.
Williams' Nico Rosberg claimed fifth spot with Ferrari number two Felipe Massa sixth, the other McLaren of Heikki Kovalainen seventh and BMW Sauber's Nick Heidfeld eighth.
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.
Countryman Rosberg, 24, has already been signed up, but the team's second driver has yet to be confirmed, although they have also been linked with Nick Heidfeld.
Germany's Nick Heidfeld, still seeking to clinch a new contract with BMW Sauber, was the biggest casualty of the first qualifying session as he could finish only 16th.
The BMW Sauber team, who currently have Robert Kubica and Nick Heidfeld as their drivers, held a meeting on Tuesday where they made the decision to quit the sport.
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