City Press reported that the church was "the latest casualty" of the migration of Afrikaans-speakers from Johannesburg's inner city suburbs.
Reverend Hennie van Rooyen told the newspaper the church was sold to Muslim buyers because its maintenance was too high.
"I wish it could've been different but we can't afford hundreds of thousands of rands to maintain the building," he said.
"And the demography of the area has changed to a predominantly Indian community."
Bishop Ryan Sooknunan, a pastor who used to rent the church for his independent Pentecostal church services, accused Van Rooyen and the Dutch Reformed Church of violating an agreement made with him by selling the church.
He threatened to take legal action and would arrange a march in protest of the sale. He also lambasted Van Rooyen's congregation for allowing a "foreign religion" to move into the building. The church grounds also contain the graves of its first minister.
Van Rooyen said the deed of sale specified that the building's historical nature would be respected.