Serguei Ivanov won the stage beating Ireland's Nicholas Roche and Team Colombia's George Hincapie who made a dash for the yellow jersey but lost out by five seconds.
Nicholas Roche
George Hincapie
Cavendish, who was well behind the stage winners sprinted to the line but was seen by the race commisaire as impeding Thor Hushovd's line.
He was docked the thirteen points he had picked up during the stage and is now eighteen points behind Hushovd in the race for the Green Jersey.
There was tragedy some 38 kilometres into the stage when a 61 year old woman was killed and two others were injured in an accident which involved a Republic Guard motorcyclist.