The Belgian, who won silver at the Tokyo Olympics in the road race and took bronze in the time trial at the Paris Games, had crashed on a paved curve during a cyclo-cross race in Mol after it snowed heavily.
The 31-year-old, who took the green jersey in the 2022 Tour de France, said he was disappointed after the fall in a statement shared by his team.
"Of course I am very disappointed to have to end my cyclo-cross season like this... my focus will now be on recovery and, later on, the preparation of the road season," said Van Aert, a three-time world champion in cyclo-cross.