SAHRC commissioner Chris Nissen, Anglican Archbishop Thabo Makgoba and other religious leaders were among those attacked on Friday morning.
The leaders were trying to negotiate a resolution to conflicts between refugees who had taken shelter at the church.
Chaos erupted while faith leaders were announcing plans for the relocation, repatriation and reintegration of the foreigners.
More than 200 refugees have been living in the church for weeks after police removed them from a makeshift camp outside the premises of the UN High Commissioner for Refugees' (UNHCR) in the CBD.

“The commission, however, cautions against this act being used as an indictment against a vulnerable group, being non-nationals — in particular asylum seekers and refugees.
“The commission calls on all within society not to use this incident or the associated occupation of UNHCR offices in Pretoria and Cape Town, by some refugees and asylum seekers, as an excuse for acts of xenophobia,” said Gushwell Brooks, commission spokesperson.
He said that the occupation of UNHCR offices did not serve the needs of asylum seekers and refugees, as resettlement was entirely based on the willingness of receiving countries of final destination.
The commission said it would continue to address the group of asylum seekers and refugees, as well as all other non-nationals in SA who were concerned about acts of xenophobia.

Source: Sowetan