This was due to an investigation into allegations against him.
Nazir Patel has been replaced by Brett Goschen, who previously headed [DATA MTN:MTN's] Nigerian business, the company said. It did not give any details on the allegations or the investigation, which it said it had commissioned.
Patel was not among the several MTN executives named in a $4.2 billion lawsuit by Turkish firm Turkcell last year. The suit, which Turkcell withdrew in May, alleged MTN used bribery and other underhanded means to obtain a licence in Iran originally awarded to Turkcell.
MTN had said the charges were false and its own internal investigation found no wrongdoing. MTN won the licence in 2005, before Patel became CFO.
Patel had been responsible for the group's financial management and accounting functions, and participated in several of its merger and acquisition activities.
MTN operates in nearly two dozen countries in Africa and the Middle East. Its shares closed unchanged in Johannesburg at 180 rand.