The Manxman fell shortly after the race rolled out of Madinat Zayed, and though he was able to remount and re-join the peloton before the official start, he wheeled to a halt again at the roadside after five kilometres and abandoned the race.
The crash appeared to have been sparked by the race director's car slowing in front of the peloton. Riders hit their brakes and several went down.
Cavendish fell on the same shoulder he fractured in the heavy crash that forced him to abandon the 2017 Tour de France. After a medical check-up, the Dimension Data team confirmed he had no shoulder injury but had suffered concussion and neck pain.
"Mark sustained a concussion and a whiplash injury after his crash today," said team doctor Adrian Rotunno. "Due to the concussion, we were not willing to risk rider safety and the call was made for Mark to stop the race. A serious neck injury has been excluded in hospital.
"He currently has some concussive symptoms and neck pain, but is otherwise stable. We will monitor Mark’s condition closely going forward."
The Abu Dhabi Tour was to be Cavendish’s third race of the 2018 season after he kicked off his campaign with a stage win at the Dubai Tour and then raced the Tour of Oman last week.