A four times winner at Spa, and with a contract extension for 2018 announced earlier in the week, Raikkonen lapped the longest track on the calendar with a best time of one minute 45.502 seconds in the closing minutes.
The 37-year-old Finn’s time was set on the quickest ultra-soft tyres, however, while Hamilton – preparing for his 200th race start – was second fastest and only 0.053 slower on the soft compound.
Hamilton was 0.092 faster than Ferrari’s world championship leader Sebastian Vettel, with the German third on the timesheets and also setting his time on the quickest but least durable tyre.
Vettel leads Hamilton by 14 points with nine rounds remaining.
Red Bull’s Dutch teenager Max Verstappen, Belgian-born and attracting a huge travelling support of orange-capped fans, was fourth fastest – also on ultra-softs – with Australian team mate Daniel Ricciardo fifth.
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Hamilton’s team mate Valtteri Bottas, who bumped into the tyre barrier after going off across the gravel and damaged his front wing, was sixth fastest.
The session was halted after 15 minutes when Brazilian Felipe Massa, who missed the previous race in Hungary after feeling dizzy in practice, crashed heavily into the tyre barrier at turn seven out of Les Combes.
He was taken to the medical centre for checks, before returning to the pitlane, with his team facing a long job rebuilding the car. The session resumed after a 10 minute stoppage.
Williams said the chassis would have to be changed and the team still hoped to get the car back out on track for some of the day’s second session, even if that looked like being optimistic.
Fernando Alonso suffered a lack of power in his McLaren, but still ended up 13th fastest. Belgian team mate Stoffel Vandoorne, who will start his home race last on Sunday thanks to a 35 place penalty due to a power unit change, was 10th.