The Frenchman survived the first mountain stage of the three-week race, defeating Rafael Valls Ferri of Spain by 57 seconds. The seventh stage of cycling's premier event took the riders 165 kilometers from Tournus to Les Rousse, a route that included three significant climbs.
Switzerland's Fabian Cancellara, who had been the overall leader for most of the first week of the Tour, finished more than 13 minutes behind Chavanel and fell far back into 58th place.
Cancellara now leads Cadel Evans of Australia by 1 minute, 25 seconds in the overall standings. Defending champion Alberto Contador is 2:26 behind in sixth place and Lance Armstrong is 14th, 3:16 behind.
Evans, Contador and Armstrong were part of a group of pre-race favorites who rode conservatively and finished Saturday's stage in a group -- 1:47 behind Chavanel.
The top of the standings is expected to undergo a major shakeup Sunday, during which the riders will make two brutal climbs at the end of the 189-kilometer stage. It will be a major test for Armstrong, whose performance on Sunday will likely show whether he can challenge for an eighth Tour de France title.