Lewis Hamilton was the fastest of the silver cars, despite a mistake-strewn final lap on a weekend when penalties mean he will start from the back.
Team-mate Nico Rosberg, who has a golden opportunity to close the title race deficit, was 0.107secs slower.
Red Bull's Daniel Ricciardo was second fastest, followed by Sebastian Vettel.
Mercedes have so far not shown their true pace on an unusual weekend that has been dominated by Hamilton's engine penalties - which amount to 55 places following three engine changes, meaning he will start right at the back - and problems with tyre choices caused by the unexpected heat.
Spa-Francorchamps is more usually associated with unpredictable and often wet weather, even in August, but this weekend has been baking, with temperatures in the low 30Cs.
That means the tyres are suffering - a problem exacerbated by the fact that greater freedom for the teams in tyre choices than previously this year has meant they have leaned towards softer tyres.
The super-soft tyre has never been brought to Spa before, because of the demands of its many long, high-speed corners.
But Ferrari picked seven sets of the tyre out of their available 13, and only one of the more durable medium.
Mercedes have gone the other way, splitting their choices much more evenly between the super-soft, soft and medium.
That meant, with only four sets of the super-soft available, Mercedes did not use it at all until the final minutes of the session.
It was not immediately clear why Rosberg was 0.768secs off Raikkonen's pace, but Hamilton had a lift in the fast double-left hander at Pouhon and then made mistakes at flat-out Blanchimont and on the entry to the final chicane.
Mercedes executive director (technical) Paddy Lowe told BBC Sport that the team were likely to give Hamilton only the least possible running in qualifying - probably meaning only one run in the first session - because of his penalties.
"We'll probably just run the minimum necessary in qualifying," Lowe said. "We want to give Lewis the strongest possible race from the back and with the maximum number of tyres."
Rosberg, despite his lack of headline pace in the final practice session, is expected to take pole, and there will be a tight battle between Red Bull and Ferrari for best of the rest.
Ricciardo's team-mate Max Verstappen, who was fastest on Friday afternoon, did only two laps on Saturday before being hit by a gearbox problem.
Hamilton is not the only driver with engine penalties.
McLaren's Fernando Alonso, who was 11th fastest and two places ahead of team-mate Jenson Button in the session, has a 35-place penalty and Sauber's Marcus Ericsson 10 places.
Belgian Grand Prix practice results
Belgian Grand Prix coverage details
Ferrari's Kimi Raikkonen set the pace in final practice at the Belgian Grand Prix as the Mercedes drivers were only fifth and seventh.