Kawasaki rider Sykes clocked a best lap of one minute 38.200, almost half a second faster than Carlos Checa in second spot on 1:38.648.
Marco Melandri was third fastest, while championship leader Max Biaggi came down in seventh place.
Biaggi's struggles - the Italian was just under a second off the pace - are a boost for Sykes, who can still win the championship at this weekend's finale should he win both races and hope Biaggi finishes outside the top six in both races.
The morning’s quickest man, Jonathan Rea, was fifth after first qualifying. Michel Fabrizio was one place up on seventh place rider Biaggi, while Leon Haslam completed the top eight.
Sylvain Guintoli was ninth and therefore the top local rider at Magny-Cours, his French compatriots Maxime Berger and Loris Baz fourteenth and fifteenth respectively.
First qualifying session times:
1. Tom Sykes (Kawasaki Racing Team) Kawasaki ZX-10R 1'38.200
2. Carlos Checa (Althea Racing) Ducati 1098R 1'38.648
3. Marco Melandri (BMW Motorrad Motorsport) BMW S1000 RR 1'38.742
4. Davide Giugliano (Althea Racing) Ducati 1098R 1'38.962
5. Jonathan Rea (Honda World Superbike Team) Honda CBR1000RR 1'39.014
6. Michel Fabrizio (BMW Motorrad Italia GoldBet) BMW S1000 RR 1'39.139
7. Max Biaggi (Aprilia Racing Team) Aprilia RSV4 Factory 1'39.144
8. Leon Haslam (BMW Motorrad Motorsport) BMW S1000 RR 1'39.149
9. Sylvain Guintoli (PATA Racing Team) Ducati 1098R 1'39.186
10. Leon Camier (FIXI Crescent Suzuki) Suzuki GSX-R1000 1'39.285
11. Eugene Laverty (Aprilia Racing Team) Aprilia RSV4 Factory 1'39.382
12. Ayrton Badovini (BMW Motorrad Italia GoldBet) BMW S1000 RR 1'39.530
13. Lorenzo Zanetti (PATA Racing Team) Ducati 1098R 1'39.709
14. Maxime Berger (Red Devils Roma) Ducati 1098R 1'39.842
15. Loris Baz (Kawasaki Racing Team) Kawasaki ZX-10R 1'39.945
16. Chaz Davies (ParkinGO MTC Racing) Aprilia RSV4 Factory 1'40.084
17. John Hopkins (FIXI Crescent Suzuki) Suzuki GSX-R1000 1'40.538
18. Hiroshi Aoyama (Honda World Superbike Team) Honda CBR1000RR 1'40.631
19. Claudio Corti (Team Pedercini) Kawasaki ZX-10R 1'40.860
20. Alexander Lundh (Team Pedercini) Kawasaki ZX-10R 1'41.535
21. Norino Brignola (Grillini Progea Superbike Team) BMW S1000 RR 1'42.990