The group of about 20 families said they left their homes in the Lisburn Road area after suffering racist attacks for almost a week.
Anna Lo, an Assembly Member for the Alliance Party in south Belfast, said the families were "very frightened".
A meeting will be held later to find emergency housing for those affected.
Bernie Kelly, from Belfast Health and Social Care Trust, said it had been a very traumatic experience for the families.
"The whole thing has escalated very quickly," she said.
"Working with the police and all the agencies together we are going to have to find a resolution."
The BBC's Mark Simpson said that in some parts of Belfast racism had become the new sectarianism.
There have been suspicions that a loyalist paramilitary group is involved in the violence, but this has been denied, our correspondent added.
One of the women who took shelter in the church, who did not want to be named, said she was very upset and scared.
She said she had feared the attackers had come to kill her and her family, and she now wanted to go back to Romania.
But the help of the church had shown a positive side to the people of Belfast as well, she added.
Earlier, the group of 115 people had tried to take refuge in a single house, but was eventually taken to the church in a police minibus.
Ms Lo said attacks on Romanian homes - which included bricks being thrown through windows - had been increasing in frequency in recent months.
"They are really very frightened," she said. "The women, when they were talking to me yesterday, they were really upset, tears in their eyes and said, 'You know we love it here, we'd like to live here, but we're too scared.'
"A woman showed me her shoulder which was quite bruised and cut across, she was hit across the shoulder."
Jolena Flett, Racial Harassment Adviser for the Northern Ireland Council for Ethnic Minorities, said they had been threatened verbally and then three properties were attacked on the same day.
"There has been an issue about the families feeling unsafe in the properties they were attacked in. What we are trying to do is provide them with alternative accommodation," she said.
Malcolm Morgan, pastor at the church, said he was happy to help and the Romanians could stay as long as they needed to.
"It's a sad indictment of our society, but hopefully we can show them a different side to Northern Ireland and a caring side of Northern Ireland," he said.
Police patrols have been stepped up in the area and officers are examining CCTV for evidence of those responsible for the attacks.
A spokeswoman for the Police Service of Northern Ireland said: "Police in the south Belfast area assisted several organisations in the temporary relocation of a number of families following consultation with community representatives.
"Families moved to a near-by church and they are being cared for by the appropriate agencies."
The families decided to leave their homes after an anti-racist rally on Monday night was attacked.
Belfast Lord Mayor Naomi Long condemned the trouble: "These kind of ugly scenes are totally unacceptable.
"A small minority of people have sadly taken away from an event which had been organised by the local community to show solidarity for their Romanian neighbours, and to express their abhorrence at their homes being subjected to racist attacks."