President Mugabe's ruling Zanu-PF party and the opposition Movement for Democratic Change (MDC) have been deadlocked in power-sharing negotiations for several months.
"The situation is truly grim. One man and his cronies - Robert Mugabe - are holding this country hostage," Mr McGee said, AP news agency reports.
Bishop Seoka said that Mr Mugabe was a "person seemingly without conscience or remorse, and a murderer".
Cholera has spread because of Zimbabwe's failing health system
"I believe it is now an opportune moment for all the church leaders to follow the retired Anglican Archbishop Desmond Tutu and the Archbishop of York, Dr John Sentamu, to call on God to cause the removal Mugabe from the office of the President of Zimbabwe," he said, calling for the prayers to be held next Tuesday.
"The church in South Africa has done this before with the apartheid regime and there is no doubt that God will hear our prayers even today."
Several African and Western leaders have recently said it was time for Mr Mugabe to step down.
Kenya's Prime Minister Raila Odinga said African countries should force him from power.
But the African Union has rejected such calls, saying a solution to Zimbabwe's problems must come from the power-sharing talks.
Bishop Seoka asked South Africans to show patience to Zimbabweans who have fled their homeland.
An estimated three million Zimbabweans are living in South Africa, and thousands cross over the border illegally every day.
More recently, hundreds have sought medical treatment because Zimbabwe's health service and water supply infrastructure have virtually collapsed.
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