The Reverend Hawu Mbatha will step down as SABC group chief executive, the corporation announced on Monday.
The SABC said its board and Mbatha had reached "an amicable arrangement" and Mbatha would be "released" from contractual obligations to "pursue his own interests".
Monday's announcement followed last week's denial by Communications Minister Ivy Matsepe-Casaburri that Mbatha would be sacked.
SABC acting senior general manager of corporate affairs, Tango Lamani, denied Mbatha had been fired. Rather, the controversial head had been "relieved" of his duties with immediate effect.
Mbatha's contract was due to have come to an end next year, Lamani said.
The SABC said Cecilia Khuzwayo, the senior general manager of human resources, had been appointed as acting group chief executive.
Khuzwayo would work closely with senior general manager of operations, Martin Slabber, and SABC chairperson Vincent Maphai.
"Dr Maphai wishes to place on record the board's appreciation of the contribution made by the Reverend Mbatha to the SABC throughout his many years of service in the corporation," the SABC said.
In a newspaper article last month, apparently based on a consultant's report, Mbatha came under harsh criticism for perceived lack of leadership.
On Monday the SABC also confirmed the resignations of executives Molefe Mokgatle and Thaninga Shope, who were found guilty by an internal disciplinary hearing for failing to comply with the corporation's financial control procedures.
The auditing firm KPMG recommended to the SABC that the two be disciplined. The firm's report found that Mokgatle had overspent on the soccer programme Dream Team, which he bought for about R42 000 per half-hour instead of the normal R27 000 per hour.
Shope failed to follow established financial procedures with her African Renaissance projects when she was general manager of SABC 2, the report stated. - Sapa