Chilton topped the times for much of the session in his Carlin machine, eventually working his times down to a 1m31.850s.
The Briton was 0.413s clear of DAMS driver Felipe Nasr, with series returnee Luca Filippi a strong third for Coloni.
Filippi, who hasn't raced at all since winning at the corresponding event last year, was half a second off the pace, having impressively topped the times on his first lap back in the car early on.
Joint points leader Davide Valsecchi was fourth fastest for DAMS, with title rival Luiz Razia down in 10th for Arden. Razia benefited from a front flap setting change halfway through the session, having languished in 16th for much of it.
Spa feature race winner Marcus Ericsson was fifth fastest, ahead of Giedo van der Garde and Esteban Gutierrez. Stefano Coletti was eighth fastest on his debut for Addax, following his switch from Coloni.
The main casualty of the session was championship contender James Calado, who lost control of the rear end of his Lotus GP machine on the exit of the Ascari chicane and thudded backwards into the tyrewall.
His car sustained some damage, but it should be fixable for qualifying in three and a half hours time. He was only 15th fastest, however.
Regular tail-ender Rodolfo Gonzalez also crashed out, spinning into the gravel at the Parabolica.
1. Max Chilton Carlin 1:31.850 14
2. Felipe Nasr DAMS 1:32.263 15
3. Luca Filippi Scuderia Coloni 1:32.391 15
4. Davide Valsecchi DAMS 1:32.401 14
5. Marcus Ericsson iSport International 1:32.410 13
6. Giedo van der Garde Catherham Racing 1:32.463 13
7. Esteban Gutierrez Lotus GP 1:32.571 15
8. Stefano Coletti Rapax 1:32.692 16
9. Nathanael Berthon Racing Engineering 1:32.830 14
10. Luiz Razia Arden International 1:32.834 14
11. Rio Haryanto Carlin 1:32.950 15
12. Julian Leal Trident Racing 1:32.954 15
13. Johnny Cecotto Barwa Addax Team 1:32.961 14
14. Fabio Onidi Scuderia Coloni 1:32.982 15
15. James Calado Lotus GP 1:33.058 11
16. Simon Trummer Arden International 1:33.084 14
17. Stephane Richelmi Trident Racing 1:33.147 14
18. Fabio Leimer Racing Engineering 1:33.149 14
19 Sergio Canamasas Venezuela GP Lazarus 1:33.352 13
20. Jolyon Palmer iSport International 1:33.471 14
21. Rodolfo Gonzalez Caterham Racing 1:33.677 10
22. Ricardo Teixeira Rapax 1:33.696 16
23. Nigel Melker Ocean Racing Technology 1:33.780 12
24. Victor Guerin Ocean Racing Technology 1:33.940 14
25. Rene Binder Venezuela GP Lazarus 1:33.977 15
26. Jake Rosenzweig Barwa Addax Team 1:34.518 12