Cecotto and championship leader Davide Valsecchi jumped to first and second just after yellow flags for an incident involving Cecotto's team-mate Josef Kral were removed.
Although a massive 0.670 seconds separated Cecotto's 1m22.075s benchmark from Valsecchi's second-placed time, the DAMS driver was using soft tyres rather than super softs like his rival.
Racing Engineering's Fabio Leimer had looked set to stay on top with his 1m22.750s as the yellow flags flew in the final minute, before swift work by the marshals allowed Cecotto and Valsecchi to stay on the accelerator on their last laps and demote Leimer to third.
Giedo van der Garde had led the way for Caterham for much of the session, but spun and tapped the barriers at Rascasse with four minutes to go, ending his morning. The Dutchman was then pushed back to fourth.
Jolyon Palmer (iSport) and early pacesetter Luiz Razia (Arden) completed the top six, ahead of Trident's Stefano Coletti, Carlin's Max Chilton (who also held first for a spell), Leimer's team-mate Nathanael Berthon, and Kral.
The latter's incident came when he spun out of the second part of the Swimming Pool and brushed the barriers.
Also in trouble were Lazarus man Giancarlo Serenelli, who spun and stalled at Rascasse, and Lotus's Esteban Gutierrez, who crashed at Sainte Devote before he could set a representative time.
1. Johnny Cecotto Barwa Addax Team 1:22.075 16
2. Davide Valsecchi DAMS 1:22.745 18
3. Fabio Leimer Racing Engineering 1:22.750 14
4. Giedo van der Garde Caterham Racing 1:22.757 12
5. Jolyon Palmer iSport International 1:22.842 17
6. Luiz Razia Arden International 1:23.104 17
7. Stefano Coletti Scuderia Coloni 1:23.343 15
8. Max Chilton Carlin 1:23.429 15
9. Nathanaël Berthon Racing Engineering 1:23.445 18
10. Josef Kral Barwa Addax Team 1:23.463 14
11. Tom Dillmann Rapax 1:23.626 16
12. Marcus Ericsson iSport International 1:24.009 14
13. James Calado Lotus GP 1:24.062 21
14. Nigel Melker Ocean Racing Technology 1:24.125 20
15. Felipe Nasr DAMS 1:24.154 19
16. Fabio Onidi Scuderia Coloni 1:24.160 18
17. Stéphane Richelmi Trident Racing 1:24.268 16
18. Julian Leal Trident Racing 1:24.315 17
19 Rodolfo Gonzalez Caterham Racing 1:24.400 17
20. Simon Trummer Arden International 1:24.629 20
21. Victor Guerin Ocean Racing Technology 1:24.868 18
22. Rio Haryanto Carlin 1:25.748 19
23. Fabrizio Crestani Venezuela GP Lazarus 1:25.827 20
24. Ricardo Teixeira Rapax 1:26.680 19
25. Giancarlo Serenelli Venezuela GP Lazarus 1:29.407 7
26. Esteban Gutiérrez Lotus GP 1:36.944 3