The blaze, which started about 1am, happened at the Wesley St house where the bodies of Anastasia Margaret Neve (35) and David Ian Clarke (49) were found inside on January 22.
The rear flat of the home had been consumed by fire when the bodies were found and the property has been abandoned since.
A man known to the couple has been charged with their murder.
A Fire and Emergency New Zealand spokesman said they were called the house at 1.15am in the morning.
Three crews, from Lookout Point, Central Dunedin and St Kilda, were called to the fire and arrived to find it well ablaze.
Extra resources were called and firefighters remained there for most of the morning.
A fire investigator had been called to look into the cause, but the fire was yet to be declared suspicious.
A police spokeswoman said the Dunedin criminal investigation branch was investigating and would be conducting a scene examination this morning.
