A warning was issued last month after the government installed a new FA president.
The suspension means that Sudan's three clubs in continental tournaments have been disqualified by the Confederation of African Football.
Al Hilal and Al Merreikh have been barred from the Champions League and Al Hilal Obeid from the Confederation Cup.
It means that Friday's two Champions League final Group A matches featuring Hilal and Merreikh will not now go ahead.
Al Merreikh had been due to face Etoile du Sahel in Tunisia this evening, with a chance of making it to the knock out stages while the already eliminated Al Hilal were supposed to be hosting Ferroviario Beira of Mozambique.
As a result of the disqualifications Ferroviario Beira will join Tunisia's Etoile du Sahel in progressing to the quarter-finals from Group A.
While in the Confederation Cup Al Hilal Obeid's final group game against Zambia's Zesco United on Sunday has also been cancelled.
Obeid had already qualified from Group C but now their opponents Zesco will play in the quarter-finals.
The winner of this weekend's other Group C game on Sunday between Angola's Recreativo do Libolo and Egypt's Smouha will go through to the last eight.
Football's world governing body Fifa has banned Sudan because of government interference in the sport.