The French time trial champion was irrepressible, 19 seconds clear of the rest of the field over the 14.75km distance.
It was a case of history repeating itself - just as in 2012 Alexander Kristoff had won the morning's penultimate stage, a short sprint, and wore the leader's jersey going into the TT.
But his 10-second lead was not nearly enough to keep Chavanel at bay - although he was able to keep second place overall, 21 seconds behind. Niki Terpstra, Chavanel's Omega Pharma-QuickStep team-mate, bagged third.
"I like to race, it doesn't matter which race," Chavanel said, already looking ahead to his next race, the Ronde van Vlaanderen.
"I like this race a lot, however. Now I have 48 hours to recover after this double victory and be ready for the race on Sunday. Last year I had a few little problems with my health during Paris-Nice. This year everything went good and normal so far. I'm in good condition. My objective is to maintain this form until Paris-Roubaix.
"As for the Ronde, I'm not one of the favourites. Sagan is strong and also Cancellara, but we have a strong, united team. We are experienced in these kind of races and also with great specialists such as Tom and Niki. The strategy will also be important. Maybe there are also a few underdogs for the race on Sunday that can surprise everyone."
Katusha rider Kristoff had been first across the line at the end of the 112.6km stage, with Modolo (Bardiani Valvole-CSF Inox) second and Elia Viviani (Cannondale Pro Cycling) third.
A five-rider breakaway had built up a 40 second lead with 25km to go, but FDJ led the effort to reel them in with 4km left and set up the sprinters to finish off the stage.
“I know the last corner was really important and my team-mates did an amazing job putting me in the right position. I then managed to keep the other guys off,” Kristoff said at the finish.
"I am very happy – all the best sprinters are here, so it is a huge satisfaction."