The bodies, which were burnt beyond recognition, have not yet been identified. Police spokesman Paul Eidenberger said it is possible that they could have been homeless people who were sleeping in the empty building.
Firefighters were called to the fire in the former Mostschenke bar and restaurant in Filmteichstrasse, not far from Oberlaa park, late on Thursday evening.
They struggled to extinguish the blaze and found the five bodies in the charred embers of the building early on Friday.
The empty building, which burnt to the ground, belonged to the Vienna city gardens department. The restaurant closed a year ago and the building is believed to have been vacant since then.
Police are now investigating the cause of the fire and autopsies on the five bodies will be carried out on Friday. "The ruins have now cooled, and we can begin our work at the crime scene," Eidenberger told media.
There have been several cases in Vienna of homeless people dying in fires - particularly in the colder months. In March a homeless man and woman died when an old wagon they were sleeping in caught fire in Floridsdorf.