Sowetan has learnt that the SAFA presidency has already begun an urgent search for Petersen's successor.
A source at SAFA, who spoke on condition of anonymity, said the knives had been out for Petersen for "some time" and his future had been discussed at executive committee meetings on numerous occasions.
"Some of the national executive members have been sharpening their knives but the man has finally opted to leave SAFA as its CEO. There are those who wanted him to go at our previous meeting.
"The relations have soured and it won't be possible for him to continue leading the organisation.
"Safa and Petersen's relationship will officially come to an end (Wednesday). Expect an announcement regarding his future and the people who will replace him."
SAFA president Kirsten Nematandani said: "I can't comment on the matter you are raising for now. That's all I can say."