"He too can be replaced, and the events of the past 15 months have shown us that we cannot rely solely on changes in the presidency to turn our country around," Makgoba said in the wee hours of Sunday when delivered a homily at the Easter Vigil in St George’s Cathedral in Cape Town.
Makgoba said he had warned against people believing that all of the country's problems could be solved by replacing one president with another.
"Changing individual leaders is no panacea for all that is wrong with governance in South Africa today," the clergy said.
Makgoba said South Africa faced a new struggle about values and institutions rather than about personalities. "We need to build strong systems which cannot be undermined by one person or party's whim.
"If we want to ensure that government works to improve the lives of all our people, especially those of the poorest of the poor, we have to strengthen our institutions," Makgoba said.
Makgoba also strongly criticised the performance of Parliament and said it had failed to hold the executive to account.
“Our people deserve a Parliament made up of members of the highest moral calibre, whether in government or in opposition,” he said, adding that “too often, the behaviour of our members of Parliament has been disgraceful.”