Anglican Archbishop Njongonkulu Ndungane prayed for "sanity" to be brought to the leadership of Zimbabwe, while Rhema Church leader Ray McCauley prayed the event would mark the beginning of momentum to help suffering people in that country.
McCauley said during a recent visit to Zimbabwe by the council he had met a woman who was a victim of operation "Drive Out Trash" and who was in tears.
"I though they were tears of suffering," he said.
"I asked why are you weeping? She said our visit was an answer to prayers that hope was there."
A convoy of trucks carrying aid relief of 4 500 blankets and 37 tons of maize, beans and oil is to leave Johannesburg for Zimbabwe on Monday.
Ndungane's office said the convoy would be escorted by members of the SA National Defence Force.
"Once in Zimbabwe, the aid will be distributed to those most in need, in and around Mutare, Bulawayo and Harare - from church halls and in resettlement camps."
Distribution would be handled by the relief arm of the Zimbabwe Council of Churches: Christian Care.
The South African embassy in Zimbabwe would help to make sure the aid gets to the appropriate distribution points.