"We recently tried on a few occasions to remedy the situation between Mr Lorgat and the board, but we have not been successful in finding a satisfactory resolution," said CSA president Chris Nenzani.
"The board unanimously felt that it was in the best interest of the organisation that we agreed to a mutual separation agreement with Mr Lorgat."
His departure comes just weeks before the start of South Africa's new Twenty20 league, the T20 Global League, which Lorgat had been responsible for setting up. It has yet to announce any television deals, reportedly raising the concern of new franchise owners, many of whom also own teams in the Indian Premier League.
Lorgat, 57, was previously chief executive of the International Cricket Council where he clashed with the Board of Control for Cricket in India (BCCI).
India objected when Cricket South Africa appointed him as their CEO in mid-2013 and have since twice curtailed tours to the country, resulting in significant financial losses to South Africa.
"I would like to thank the board for their wholesome support during my time, especially in my early years at CSA. It is most unfortunate that we must part ways in this manner, but it is the best way forward for CSA," said Lorgat in a statement.
CSA vice president Thabang Moroe will stand in for Lorgat until a successor is found.
(Reporting by Mark Gleeson; Editing by Christian Radnedge)
