Nonkonyana was suspended by local football's controlling body in October last year following his comments that Bafana Bafana coach Gordon Igesund should be fired if he fails to win the 2014 African Nations Championship (Chan).
Due to his suspension, Nonkonyana was also asked to vacate his position as the chairman of Chan organising committee, and was replaced by Molefi Oliphant.
SAFA said today that Nonkonyana was invited to explain himself to the congress, but instead opted for the legal route.
By taking SAFA to courts, it was noted that Nonkonyana violated a fundamental football constitution hence his dismissal.
As a matter of fact, Nonkonyana went to court seeking an interdict to have the agenda of his removal erased from the Annual General Meeting which failed.