Coach Stuart Baxter (65) has resigned from the job despite having three years left on his contract.
They were eliminated by Nigeria in the last eight.
He won eight, lost eight and drew four of the matches he was in charge of as coach.
The former Kaizer Chiefs and SuperSport United coach was out of the country since Bafana’s return from Afcon and had been expected to deliver his Afcon report, but that was delayed.
The fact that he had called a personal press conference was a clear indication that he was on his way out.
He said at the conference that he believed he had done as much as it was possible to do and achieve as the coach, but that South Africa still had a long way to go with its football.
“Someone should continue with this project and therefore I am resigning,” he said. “It was my personal decision,” he made clear.
“There is no monetary settlement. This had nothing to do about money. The figures quoted about my salary have been embarrassingly way off the mark,” he added.
In the press conference, he also revealed that he had delayed a biopsy to test for cancer so that he could travel with the team to Libya, as their “best chance to make Afcon”, which he put forward as evidence of his total commitment to his job.
Baxter was born in England of Scottish parentage, and brought up in both countries.
He played professionally for a number of clubs in England, Scotland, Australia, Sweden and in the United States.
He has previously managed clubs in Sweden, Norway, Portugal, Japan and South Africa. In international football, he has managed South Africa twice as well as Finland and the England under-19 team.