He set a time of two minutes 11.389 seconds, half a second faster than Pastor Maldonado of Williams in second.
Toro Rosso pair Daniel Ricciardo and Jean-Eric Vergne followed, with 0.8s between the two.
However the timesheets have little meaning given the constant rain at the Ardennes circuit, famed for its changeable weather conditions.
Michael Schumacher, competing in his 300th grand prix this weekend, suffered a heart-stopping high-speed slide at Eau Rouge but managed to regain control of his Mercedes.
"There's so much water out there, going into and out of Eau Rouge. It's pretty dangerous out there," said Force India's Nico Hulkenberg.
Several drivers including Mark Webber and Jenson Button had to use the escape road at Les Combes as they struggled to guide their cars round the corner at the bottom of the hill.
Webber was the highest-placed leading driver for Red Bull in fifth with team-mate Sebastian Vettel ninth. They completed 13 and 12 laps respectively.
Lewis Hamilton and Button were 15th and 16th in the McLarens having completed only eight and five laps respectively with standings leader Fernando Alonso of Ferrari 22nd - half a minute down, having evidently decided not to go after a competitive time - after only four laps.
Felipe Massa was left stranded with seeming engine failure at Bus Stop after the chequered flag, with stewards wheeling the F2012 away once the smoke had dissipated.
The teams will hope for better conditions in the afternoon session as McLaren and Red look to take the fight to Ferrari after the mid-season break.
- Daniel Ricciardo
- Pastor Maldonado
- Michael Schumacher