The Finn clocked a time of one minute 49.465 seconds, with Australian Daniel Ricciardo second and 0.268 slower for champions Red Bull.
Mercedes had finished one-two in the previous two Spa practise sessions.
Formula One leader Nico Rosberg was third fastest for Mercedes, with title rival and team mate Lewis Hamilton fifth and with exactly the same time of 1:49.817 as Ferrari's four times Spa winner Kimi Raikkonen.
Rosberg leads 2008 champion Hamilton by 11 points after 11 of the 19 races.
Hamilton, who was fastest on Friday, and Rosberg had led the timesheets until about five minutes to the end with the pair separated by only a thousandth of a second.
Rosberg has yet to finish on the podium at Spa, while Hamilton won in 2010, but the Mercedes powered cars - which include Williams, Force India and McLaren as well as the works team - are expected to dominate.
With the circuit damp but drying as the session started, drivers left it late to venture out for meaningful laps. Qualifying later could also be wet.
(Reporting by Alan Baldwin; Editing by John O'Brien)
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