The man fled the scene of the burning shop front with another person in a white ute, on the outskirts of Melbourne's northwest, about 3am on Thursday.
Moments earlier, he had set his arm alight, while a third man suffered significant burns to his body.
That man, aged in his 20s, was left at the scene and is fighting for life after being found nearby by emergency services.
Burnt clothing, including a single Nike shoe could be seen in the carpark of the The Boss tobacco store on Thursday.
There have been more than 150 tobacco store fires in Victoria since March 2023.
A Victoria Police spokesperson said the exact circumstances surrounding the latest fire are still being determined.
The fire is being treated as targeted.
Police believe the ute pulled up outside the shop early Thursday before three people left the car and entered the shop.
"It appears accelerant was poured in the premises and it was set alight," the spokesperson said.
"Two people have subsequently suffered burns as a result of the blaze, including the man who was later located nearby."
The ute was later found on fire in Hopetoun Park, about 9km away, and has been seized for forensic testing.
Police are still trying to identify and locate the two other people involved, and believe one of them has significant burns to their hands and feet.
''We have said repeatedly that deliberately lighting fires comes with immense risk, not only to the broader community but also to the offenders involved," Arson and Explosives Squad Detective Inspector Chris Murray said.
''We have also seen incidents where offenders have died as a result of sustaining burns and this remains a very real possibility to happen again with this incident."
Detectives remained at the scene on Thursday, with sections of Melton's High Street sectioned off.
The front of the store, which had its black roller door down at the time, can be seen damaged by fire.
The Gang Crime Squad, formerly Taskforce Lunar, has executed more than 350 raids and made at least 212 arrests for offending connected to crime groups involved in the illegal tobacco trade.
More than $50 million worth of cash, illegal cigarettes, tobacco and vapes has also been seized from tobacco retailers.
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