There were six participating teams in the Santam Bank Trophy Division A. Teams played each other twice over the course of the season, once at home and once away. Teams received two points for a win and one points for a draw. The top two teams in the division – along with the top two teams from Division B qualified for the title play-off finals. The team that finished first in Division A would play at home against the team that finished second in Division B and the team that finished second in Division A would play at home against the team that finished first in Division B.
The Division A champion qualified for the promotion play-offs. That team played off against the team placed sixth in the Currie Cup Division B over two legs. The winner over these two ties qualified for the 1990 Currie Cup Division B, while the losing team qualified for the 1990 Santam Bank Trophy.
In the promotion play-offs, Eastern Free State conceded the second leg to Boland, who won promotion to the Currie Cup 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.[30]
In the relegation play-offs, South Western Districts beat Northern Natal on aggregate and won promotion to Division A. However, due to the withdrawal of South West Africa and the Currie Cup Division B being expanded from six teams to eight teams, only nine teams were left in the Santam Bank Trophy and it was decided to merge Division A and Division B into a single division for 1990.