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The Finn clocked 1min49.465; Daniel Ricciardo was second and 0.268 slower for Red Bull after Mercedes finished 1-2 in the first two practice sessions.
F1leader Nico Rosberg was third-fastest for Mercedes with title rival and team mate Lewis Hamilton fifth on exactly the same time - 1min49.817 - as Ferrari's four-times Spa winner Kimi Raikkonen.
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Rosberg leads 2008 champion Hamilton by 11 points after 11 of the 19 races.
Hamilton, fastest on Friday, and Rosberg had led the time sheets until about five minutes to the end of third practice with the pair separated by only a thousandth of a second.
Rosberg has yet to finish on the Spa podium; Hamilton won in 2010 but the Mercedes-powered teams - Williams, Force India, McLaren and 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.
Final free practice ahead of the 2014 Belgian F1 GP at Spa-Francorchamps
1 Valtteri Bottas (Finland) Williams-Mercedes 1min49.465
2 Daniel Ricciardo (Australia) Red Bull - Renault 1min49.733
3 Nico Rosberg (Germany) Mercedes 1min49.739
4 Kimi Raikkonen (Finland) Ferrari 1min49.817
5 Lewis Hamilton (Britain) Mercedes 1min49.817
6 Fernando Alonso (Spain) Ferrari 1min49.890
7 Daniil Kvyat (Russia) Toro Rosso - Renault 1min49.893
8 Jenson Button (Britain) McLaren 1min50.203
9 Felipe Massa (Brazil) Williams-Mercedes 1min50.423
10 Jean-Eric Vergne (France) Toro Rosso - Renault 1min50.535
11 Sergio Perez (Mexico) Force India - Mercedes 1min50.592
12 Kevin Magnussen (Denmark) McLaren 1min50.748
13 Sebastian Vettel (Germany) Red Bull - Renault 1min50.814
14 Nico Hulkenberg (Germany) Force India - Mercedes 1min50.866
15 Adrian Sutil (Germany) Sauber - Ferrari 1min50.962
16 Romain Grosjean (France) Lotus - Renault 1min51.509
17 Pastor Maldonado (Venezuela) Lotus - Renault 1min51.610
18 Esteban Gutierrez (Mexico) Sauber - Ferrari 1min51.898
19 Jules Bianchi (France) Marussia - Ferrari 1min52.457
20 Max Chilton (Britain) Marussia - Ferrari 1min52.984
21 Marcus Ericsson (Sweden) Caterham - Renault 1min54.294
22 Andre Lotterer (Germany) Caterham - Renault 1min55.008