The 29-year-old Briton, who was second behind Rosberg in the morning session, clocked a best lap of one minute and 49.189 to finish clear at the top of the times on a typically incident-filled day at the old Spa-Francorchamps circuit in the Belgian Ardennes.
Rosberg was six-tenths of a second slower than Hamilton to finish second ahead of two-time champion Fernando Alonso of Ferrari, William's Felipe Massa and Jenson Button of McLaren on a rare dry day at the track.
Valtteri Bottas was sixth for Williams ahead of Russian rookie Daniil Kvyat of Toro Rosso, Australian Daniel Ricciardo for Red Bull, Danish rookie Kevin Magnussen in the second McLaren and Nico Hulkenberg for Force India.
The session began under a heavy black cloud and produced two major 'red flag' accidents, but nobody without anyone being injured.
The first came when Venezuelan Pastor Maldonado lost control of his Lotus car in the approach to Pouhon and hit the barriers heavily.
He was quickly in communication with the team via radio to say he was unhurt, but his car was seriously damaged and he was out for the rest of the session.
The second red flag came when Mexican Esteban Gutierrez spun off at Blanchimont in his Sauber.
"Can you get back to the garage?" the team asked him. "It is the gear box...Something break completely," he replied.
In the intervening periods of on-track action, Alonso clocked 1:51.693 to go top before Hamilton, who was second behind Rosberg in the morning practice session, regained the ascendancy by taking half a second out of the Spaniard's best time.

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