Police blocked off four CBD blocks shortly after 2pm, but Flinders Street was reopened to traffic about 90 minutes later. Nobody was injured.
The man was charged overnight with reckless conduct endangering life and a number of traffic offences.
He was remanded in custody and will appear at the Melbourne Magistrates Court on Thursday morning.
On Wednesday, Victoria Police Superintendent Dan Trimble said the man was not armed and police did not believe the incident was related to terrorism.
The man had a backpack in his car, prompting police to send in the bomb response unit but they found no threat.
Police were not able to say if the man was affected by drugs or alcohol. Mr Trimble said the actions could “quite possibly” have been the result of a mental health episode.
Mr Trimble said when police were notified of the incident they were “absolutely” concerned by the possibility of another incident similar to the Bourke Street tragedy perpetrated by James Gargasoulas.
“Any behaviour where erratic driving is involved is always dangerous, particular at a busy intersection,” he said.
When asked if Victoria Police would consider new ways to patrol the intersection, a police spokeswoman said the force was “constantly assessing the way it responds to incidents”.
– With Simone Fox Koob, Paul Sakkal and Michael Fowler
Rachel is a breaking news reporter for The Age.