Most Rev Thabo Makgoba and other church leaders asked some of the migrants to leave Cape Town's Methodist Church on Friday due to overcrowding.
The migrants, mostly from other African countries, were staging a sit-in in the church after being forced to leave the offices of the UN's refugee agency (UNHCR) in Cape Town two weeks prior.
The crowd demanded that they be resettled in another country and be given refugee status as they don't feel safe in South Africa due to a recent spike in xenophobic violence.
JP Balous, a man speaking on behalf of the refugees told a local news channel that they have "been treated like rubbish".
"We are human beings, we came here to seek refuge... The human rights commission is actually the human rights abuse in South Africa," he said.
Video aired by broadcaster eNCA showed a fight breaking out in the church, injuring Archbishop Thabo and South Africa's Human Rights Commissioner Chris Nissen.
Witnesses said the fight started after a Congolese church leader had the microphone snatched out of his hand and was beaten up by an angry crowd.
"They started throwing papers at me when I was trying to calm them down," Archbishop Thabo told eNCA.
"One doesn't expect violence to break out at a sanctuary," the archbishop told TimesLive. "We are dealing with a human issue here, a desperate situation."
Archbishop Thabo tried to make light of his small injury.
He told Times Live: "At least my wife likes the tiny injury on my forehead. She calls it a dimple."
The Refugee Alliance for Justice has urged department of Home Affairs to take action on the issue.
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