Hayatou was accompanied by four CAF executive members and local soccer bosses Kirsten Nematandani and Danny Jordaan, the presidency said.
"At the meeting, President Zuma thanked CAF for entrusting South Africa with hosting the Orange Africa Cup of Nations (AFCON) 2013 tournament."
Zuma also urged the nation to rally behind the four remaining teams.
Hayatou thanked South Africa for coming to Africa's rescue by hosting the tournament when Libya could no longer do so.
He also thanked the country for being a reliable partner and supporter of African football.
Nematandani, who is president of the SA Football Association, said 800 000 tickets had been sold for the tournament, exceeding expected sales of 500 000.