On a split stage day, Alexander Kristoff (Katusha) had earlier won stage 3a thanks to a sprint finish victory in De Panne.
It was stage 3b though that would decide the race – a 14.7km individual time trial also in De Panne.
Chavanel completed the course in 17:49 which saw him move from 12th to first in General Classification.
Lieuwe Westra (Vacansoleil-DCM Pro Cycling Team) finished four seconds back which saw him finish second in both the stage and the overall standings.
Svein Tuft (GreenEdge) was third in the stage with Maciej Bodnar's (Liquigas-Cannondale) fifth place finish in the ITT enough to see him reach the overall podium.
Kristoff had gone into the time trial as the overall leader after his win earlier in the day but never challenged in the time trial.
"I am super happy with this victory," Chavanel said.
"This year I did not win until now, and a lot of our riders have already won. It was a little disappointing that I was riding well but unable to win a race. I am also happy because this victory came at a time trial. I worked a lot during the winter in the time trial because, in the past, I was a three-time French champion time trialist. I used to be a good rider for the time trial, but in the last year, because of my back problem, I wasn't able to perform well.
"This winter I worked a lot on my position with the team staff and Specialized staff, now we start to see some results. I was 4th in Argentina, 6th in the Stage 1 Paris-Nice time trial, so I am reaching my objectives with my time trial bike."