Once at the scene police say the man who emerged from the auto attacked officers, before members of the public alerted them to several people who had been stabbed.
The two survivors were taken to hospital - one in a suspected critical condition. Hindustan Times, owned by HT Media Ltd, is one of India's largest publications that provides unbiased news, analysis and features on politics, sports, entertainment, lifestyle and more. "A third person has also been taken to hospital".
Victoria Police confirmed the man has died and had links to convicted terror plotters.
Only after he was shot did police realize that three members of the public, all men, had been stabbed.
"There is no known link to terrorism at this stage", Clayton added.
Victoria state premier Daniel Andrews said the attack was "an evil and terrifying thing that has happened in our city and state today".
Other people on the scene threw chairs and tried to ram a shopping trolley into the attacker to take him out.
Victoria State Police Chief Commissioner Graham Ashton told a press conference that the male assailant stabbed three men before one of the responding police officers shot him once in the chest at the scene. He later died in hospital while under armed guard.
Witnesses said the man had parked a vehicle on Bourke Street, a busy shopping area in Australia's second-largest city, before it was seen in flames.
It was too early to say if the incident was terror-related, they said.
Markel said bystanders were yelling out "just shoot him, just shoot him", while police officers were trying to disarm the attacker. Police are asking for members of the public to avoid the area.
Streets were closed, trams halted and nearby buildings evacuated as police rushed to the scene, which was crowded with shoppers and commuters late on Friday afternoon local time.
The street where the auto caught fire was the scene in January 2017 of a fatal incident in which a man drove his vehicle at pedestrians at high speed, killing six people and wounding about 30.
Premier of Victoria Daniel Andrews has described the attack as an "evil and bad thing", while also praising the fearless people who were involved in the frightening incident.