The 24-year-old Briton, who was fastest Friday and will be chasing his third Hungarian pole in a row, produced the quickest time of the weekend so far with a lap of one minute, 21.009 seconds.
Neither Hamilton nor Finnish team mate Heikki Kovalainen [ Images ] have stood on the podium this season after spending the first half of the year struggling with an uncompetitive car. Kovalainen won in Budapest last year and led Friday's first session.
However, the Mercedes-powered team have made significant improvements in the past month and are hoping to be back in the running after Brawn and Red Bull dominated the first nine rounds.
Brawn's championship leader Jenson Button [ Images ], who won six of the first seven races and is 21 points clear in the standings, had hoped to be back to form in the Hungarian heat but lapped only 17th quickest in the final practice before qualifying.
His Brazilian team mate Rubens Barrichello [ Images ] was 13th.
Red Bull's Mark Webber [ Images ], who took his first win in 130 starts at this month's German Grand Prix, was ninth on the timesheets with German team mate Sebastian Vettel [ Images ] 10th. Vettel is second in the championship.
Ferrari's [ Images ] Felipe Massa [ Images ], who had victory snatched from his grasp by a late engine failure in Hungary last year, lapped seventh quickest and the Italian team seemed to struggle on the twisty track.
Spanish new boy Jaime Alguersuari put in another solid performance for Toro Rosso, lapping quicker than both the Force India [ Images ] drivers and again keeping out of trouble in his 20 laps.
The 19-year-old will become the youngest driver to start a race Sunday.
Force India's Adrian Sutil [ Images ] ended the session 15 minutes early after he ploughed into the tyre wall, leaving his mechanics with work to do before qualifying.