After championship leader Rosberg had set the pace in the morning with a lap just 0.097 seconds faster than the Briton's best, Hamilton turned the tables after lunch with a substantially quicker effort.
The time of one minute 49.189 was 0.604 better than Rosberg's on a cloudy but bright day at the longest track on the calendar, where the weather can combine the seasons in the space of an afternoon.
Rosberg had topped the first session timesheets in 1:51.577 as the two title rivals - separated by just 11 points after 11 of 19 races - renewed their duel after the August break with their domination intact.
The afternoon running was interrupted when Venezuelan Pastor Maldonado crashed his Lotus into the barriers on the way to Pouhon.
There was a further stoppage in the first half hour when Mexican Esteban Gutierrez's Sauber spun and was stranded on the track at Blanchimont.
The Mercedes-powered teams were predicted to dominate and had seven cars in the top 10 in the opening session.
But Ferrari's showing, with four times Spa winner Kimi Raikkonen fifth fastest in the morning despite a spin at La Source, indicated they would not have it all their own way.
Williams had a low-key start, with Finland's Valtteri Bottas 10th on the timesheets and Brazilian Felipe Massa 15th, but picked up with Massa fourth in the afternoon.
Red Bull's Daniel Ricciardo, winner of the previous race in Hungary, was ninth and eighth in the two sessions while his quadruple world champion team mate Sebastian Vettel sat out the second session due to an electrical problem that forced an engine change.
At the bottom end of the field, Germany's Andre Lotterer limbered up for his F1 debut with Caterham as a replacement for Japan's Kamui Kobayashi by lapping faster than Swedish rookie team mate Marcus Ericsson in the morning.
American Alexander Rossi replaced Max Chilton for the session at Marussia but his hopes of completing the weekend and racing for the first time evaporated when the Briton was reinstated following contractual wrangles.
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