Van Hooydonck was severely injured in the crash and was in a critical condition, Belgian newspaper Het Nieuwsblad said.
"We can confirm that earlier today our rider Nathan van Hooydonck became unwell while driving his car, leading to his involvement in a traffic accident," a team statement said.
"He was subsequently transported to hospital, where he is receiving good medical care.
"We cannot confirm rumours that his condition is critical. He is undergoing further medical examinations. Thank you all for your messages to Nathan and the team."
Van Hooydonck was waiting at a junction in the town of Kalhmthout, near Antwerp, with his pregnant wife in the passenger seat when he became unwell and inadvertently accelerated into traffic.
"A car with two occupants was waiting at the traffic lights at the intersection of Dorpsstraat and Kapelsesteenweg," Patrick De Smedt, spokesperson for the border police zone, was quoted as saying by Het Nieuwsblad.
"The driver was resuscitated on site and taken to hospital in life-threatening condition.
"His pregnant wife who was sitting next to him was not injured but was also taken to hospital for a check-up."
Later on Tuesday Jonas Vingegaard, Van Hooydonck's teammate at Jumbo-Visma, won the 16th stage of the Vuelta a Espana, looking emotional as he crossed the line.
But Attila Valter, also of Jumbo-Visma, offered better news after the stage.
"We just heard on the team radio that Nathan is awake and is okay, that's what we were hoping for," the Hungarian said. "I hope he is watching that this victory is for him."
Van Hooydonck, who turned pro with BMC in 2017, has been with Dutch outfit Jumbo-Visma since 2021.
He was part of the team supporting winner Vingegaard at this year's Tour de France and last week rode in the Tour of Britain and was set to represent Belgium at the upcoming European road championships.