Offenders emerged from a stolen white Toyota Hiace van outside the stores on Buckingham Avenue at Springvale in Melbourne's southeast just before 2am on Thursday.
The crooks used the van to break the window of one premises before it was rammed into the second one about three shopfronts away and both were set alight.
Residents in the 20 apartments above the stores were forced to evacuate after the "intense" fire cut their power.
While the buildings sustained significant structural damage, no one was physically injured, police confirmed.
The fire is being treated as suspicious and investigators suspect an attempted arson attack on the same stores in October was linked to their sale of illicit tobacco.
Detectives from Taskforce Lunar, which was set up to investigate crime groups involved in the illicit tobacco trade, are investigating the circumstances.
"We've discovered evidence at one of those premises that illicit products, including vapes, were being sold," Taskforce Lunar Detective Inspector Graham Banks said on Thursday.
Police are waiting to view CCTV footage to see how many suspects were involved because the power was cut to one of the buildings.
But Det Insp Banks issued a warning to landlords about knowing who they were renting their shopfronts to.
"There are landlords out there who are well aware, some would be suspect, and others that haven't inquired into the fact that they're having illicit products sold on their premises," he told reporters.
"This is putting that premise at risk, but also neighbouring premises.Â
"It's bad enough when other businesses are closed down due to these arsons, but we're going to see an instance, I'm sure, where a person is killed."
Landlords who police suspect owned premises rented to illicit tobacco businesses were contacted by their local councils in May, Det Insp Banks said.
"Without these shopfronts operating, we wouldn't see the arsons," he said.
"If their insurance claim is made, police will speak very candidly to the insurance provider about what communications have or haven't been sent to those premises."
More than 125 fires involving tobacco stores are being investigated and police have arrested over 100 people in connection.
Residents in apartments above the stores have been allowed back into their homes to assess the damage sustained.
