There were six participating teams in the Santam Bank Trophy Division A.
The bottom team on the log qualified for the relegation play-offs.
The winner over these two ties qualified for the 1990 Santam Bank Trophy Division A, while the losing team qualified for the 1989 Santam Bank Trophy Division B.
Eastern Free State were initially relegated, but due to the Currie Cup Division B's expansion to 8 teams, they retained their place.
In the relegation play-offs, South Western Districts beat Northern Natal on aggregate and won promotion to Division A.