Cavendish was involved in an incident shortly after the stage start in Stoke-on-Trent. Although he got back on his bike and continued with the stage, he later withdrew.
No detail of any injury has been released by either the race's organiser or his Etixx-QuickStep team, although both confirmed his withdrawal.
Cavendish's wife, Peta, later tweeted that she had spoken to the Manx rider and that his injuries "could have been a lot worse".
Cavendish was also involved in a crash with Spanish rider Gorka Izagirre during the previous day's stage.
Cavendish had been one of the leading favourites to win the final two stages in Ipswich and London.
The news of Cavendish's withdrawal from the race coincided with the announcement from British Cycling that Cavendish had been selected to ride for Great Britain in the 2015 World Championships road race on September 27.
The course in Richmond, USA, seems to suit Cavendish, and it is thought he is one of the nominated leaders of the GB team. It is unclear whether Cavendish's injuries will have any bearing on his Worlds appearance.
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