The group, known as Iffley Open House, had previously occupied a former car showroom on Iffley Road, owned by Wadham College, on New Year's Eve.
They were asked to leave and then moved into the disused Osney Mill site in February.
The university said the former power station was unsafe won a  court order to evict the group.
Creative Solutions
It added that the building was due to be redeveloped by the Said Business School.
Some of the squatters said they were offered sleeping space at a local church, but most will now be back on the streets, the group said.
Volunteer Miranda Shaw said: "One good thing is that it has created enough of a stir that there are big conversations happening.
"We will be coming together in the coming weeks to meet churches, councils, the university, service providers and police.  There is the intention to find creative solutions."
Oxford University has always maintained that it is sympathetic to plight of the homeless and has been working towards resolving the situation.
Squatters who had taken over a disused power station owned by Oxford University have vacated the building.