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.