Mark Cavendish accused Peter Sagan of elbowing him into the barriers around 200 metres from the stage four finishing line in Vittel on Tuesday.
World champion Sagan was initially docked 30 seconds but that punishment has since increased, with organisers disqualifying him from the event.
The Dimension Data sprinter will himself play no further part, though, as the injury sustained in the crash has turned out to be as bad as he initially feared.
After completing the race several minutes behind winner Arnaud Demare, Cavendish underwent a scan which revealed that he has broken his shoulder – the same one that he dislocated when crashing out of the Tour on the opening stage three years ago.
Only Eddy Merckx has won more Tour stages than the Brit, who has 30 to his name in all.