Van Aert, 24, appeared to take a corner too close to the barriers, catching his shoulder before coming off the bike at speed with just over a kilometre of the 27.2km circuit to go.
The Jumbo Visma rider has successfully undergone surgery after suffering a "deep flesh wound" to his upper right leg - and he will now face a two-month rehabilitation programme in which he will not be allowed back on the bike.
Pidcock claims win at Brabantse Pijl beating Van Aert in sprint finish
Highlights: Pinot, Alaphilippe seal French one-two as Thomas loses ground
Mathieu Heijboer, Head of performance for the Dutch team, said:
He was operated on by the surgeon. He stitched the capsule and skin and cleaned everything well. He has to stay in hospital for a few days.
Van Aert received immediate treatment from team medics roadside, and fears for his wellbeing were raised when sponsorship banners were used as a makeshift tent while he was tended to.
However, his team later confirmed that while he had abandoned the race, he was conscious after suffering a flesh wound seemingly allaying initial concerns that he had suffered more severe injuries.
Van Aert was fighting for the provisional stage lead in the time trial against his countryman Thomas De Gendt.
Nico Verhoeven, Jumbo-Visma team director, added: “The surgeon talked about a two-month rehabilitation period in which he would not be allowed to cycle. But Wout saw it differently. A cyclist normally recovers faster.
We are still waiting to hear when he can start his cyclocross season. Although, we are not working on that now. Let us hope that he recovers 100 per cent.
Tour of Flanders
Van Aert urged to find that 'one thing you specialise in'
Ronde van Vlaanderen
The power of the mind: How Asgreen edged Van der Poel to conquer Flanders