Van der Poel, who has won a stage on the Tour de France and Giro d'Italia, has been left "shattered" according to his Team Alpecin-Deceuninck boss Christoph Roodhooft.
"He didn't sleep all night and was mentally a bit broken as well," Roodhooft told reporters.
"He was expecting a lot of this day (race) and did all he could in the last two months after his bad Tour de France. He had found joy and happiness again in cycling and was hoping to have a nice race today."
Speaking to Belgian sports website Sporza, the two-time Tour of Flanders winner and four-time cyclocross world champion said he had confronted two children who were knocking on his hotel room door "continuously".
"I went to bed early and many children in the hallway of my room found it necessary to knock on the door," he said. "After a few times I was done with it. I did not kindly ask to stop. Then the police were called."
Van der Poel added that after he was charged he did not return to his hotel room until 4am local time.
New South Wales police said Van der Poel had been arrested at the Grand Parade Brighton-Le-Sands in Sydney on Saturday evening and granted conditional bail to appear at Sutherland Local Court on Tuesday.
"He was allegedly involved in a verbal altercation with two teenage girls – aged 13 and 14," a NSW police statement said. "It's further alleged the man then pushed both teenagers, with one falling to the ground and the other being pushed into a wall, causing a minor graze to her elbow.
"Hotel management were notified of the incident who then called police."
Sunday's elite men's race was won in emphatic fashion by Evenepoel, who finished two minutes and 21 seconds ahead of France's Christophe Laporte having gone clear with 25km remaining. Evenepoel becomes the first rider since Bernard Hinault in 1980 to win a grand tour, a monument and the rainbow jersey in the same season.
The 22-year-old became Belgium's first grand tour champion in 44 years when he won the Vuelta a Espana a few weeks ago. He won the Liege-Bastogne-Liege monument race earlier this year.