The crash occurred in the neutral zone section of stage 1.
Team doctor Adrian Rotunno said: "Mark sustained a concussion and a whiplash injury after his crash today".
It is not yet clear how serious the 32-year-old's Manxman's injury is.
"It makes it a long time racing in the Middle East, but it's an honour to come back to Abu Dhabi", Cavendish told media during the top rider press conference on Tuesday.
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VeloNews confirmed with the race organization that the race director's auto braked and caused the crash, in which four riders went down.
Jaco Venter will be the lone South African in the Team Dimension Data for Qhubeka squad for the Abu Dhabi Tour which starts on Wednesday, 21 September. He now has some concussive symptoms and neck pain but is otherwise stable.
He was forced to withdraw from the 2017 Tour de France when he fell and fractured his right shoulder.
The team weren't willing to allow Cavendish to continue due to the concussion, and will continue to monitor his condition.