Webber had been quickest in both of Friday's sessions as he erased memories of his disappointing weekend at his home Australian Grand Prix two weeks ago.
Hamilton's McLaren team-mate Jenson Button, the 2009 champion, was third fastest ahead of Germans Nick Heidfeld in a Renault and glitch-plagued reigning champion Sebastian Vettel in the other Red Bull.
Vettel concentrated on race preparation, but has a problem with his moveable rear wing and also lost a television camera that was attached to his car.
Two-time champion Fernando Alonso was sixth fastest for Ferrari, after struggling for pace during most of the session.
Russian Vitaly Petrov, who finished a remarkable third for Renault in Melbourne, was seventh ahead of Brazilian Felipe Massa in the second Ferrari and Japan's Kamui Kobayashi of Sauber.
Seven-time champion Michael Schumacher of Germany, now 42, was 10th for Mercedes ahead of his team-mate compatriot Nico Rosberg.
The session was run in hot and humid conditions with the air temperature rising to 34 degrees Celsius and the track temperature touching 40 degrees.
Higher temperatures were forecast for the qualifying laps to be held on Saturday afternoon, ahead of Sunday's race.