Cavendish, who won six stages last year and four the previous year, had looked below par since the beginning of the Tour, crashing in the first stage to Brussels and being out-sprinted by Alessandro Petacchi on Wednesday.
The 25-year-old Briton, who was hampered by a dental infection at the start of the season, finally set his doubts aside after great work by his Columbia team mates on Thursday.
Germany's Gerald Ciolek was second and Norway's Edvald Boasson-Hagen came home third.
It was Cavendish's fourth victory this season and the 57th in his career.
Swiss Fabian Cancellara retained the overall leader's yellow jersey after a reasonably quiet ride in hot and sunny weather.
A three-man break involving Spanish champion Jose Ivan Guttierez, Belgian Jurgen van de Walle and France's Julien El Fares was thwarted with three kilometers to go.
