The Williams driver was quickest with a time of one minute 49.465 seconds in damp conditions at Spa-Francorchamps after Mercedes duo Nico Rosberg and Lewis Hamilton had topped the timesheets in the first and second sessions on Friday.
Red Bull's Daniel Ricciardo was second fastest, with Rosberg third, Kimi Raikkonen fourth and Hamilton down in fifth as he attempts to cut the gap to his team-mate in the battle for the drivers' championship.
Fernando Alonso was sixth after finishing third in both sessions in his Ferrari on Friday.
Only three cars posted times in the first half an hour of the session due to a wet track, but as conditions improved drivers were able to head out on soft tyres in the closing stages and it was Bottas who made a statement of intent.
Red Bull's Ricciardo snatched second - 0.268secs slower than Bottas - right at the end of the session to push championship leader Rosberg down a place.
Less than half a second covered the top seven cars and Mercedes will be hoping normal service is resumed in qualifying.