There were six participating teams in the Santam Bank Trophy Division A. These teams were split into two sections of three teams each. Teams played the teams in their own section once over the course of the season and teams in the other section twice, once at home and once away. Teams received two points for a win and one points for a draw. The top team qualified for the Division A section finals, played at the home venue of the higher-placed team, as well as the Division A finals.
The bottom team on the log with the worst record in their group qualified for the relegation play-offs. That team played off against the team that won the Santam Bank Trophy Division B over two legs. The winner over these two ties qualified for the 1989 Santam Bank Trophy Division A, while the losing team qualified for the 1989 Santam Bank Trophy Division B.
North Eastern Cape qualified for the Division A Title Play-Off Final game and the Trophy Finals Semi-Final. Northern Natal qualified for the Promotion/Relegation Play-Off game.
* Legend: Pos = Position, Pl = Played, W = Won, D = Drawn, L = Lost, PF = Points For, PA = Points Against, PD = Points Difference, TF = Tries For, TA = Tries Against, Pts = Log Points
Points breakdown: *2 points for a win *1 point for a draw
In the relegation play-offs, Northern Natal conceded the second leg to Far North, who won promotion to the Division A. Northern Natal were initially relegated to Division B, but due to the Currie Cup Division A's expansion to 8 teams, they retained their place.[4]