The Belgian champion and Olympic silver medalist stopped training on the Ronde course on Thursday.
Van Aert had been in excellent form so far this spring, the 27-year-old recently won the E3 one-day race in his home country of Belgium around Harelbeke.
At the end of February, van Art had already won the Omloop Het Nieuwsblad race in East Flanders.
Both of the “Tour of Flanders” have become Zweiter from Aert 2020.
Jumbo duo celebrates double victory: Van Aert triumphs – highlights