Cape Town City defeated Leicesterford City 4-2 at the Dobsonville Stadium in a game that had four penalties, two for each side, while Milford played to a 0-0 draw at Hungry Lions in a game played in Upington.
The Mother City club finish in second place in the table behind automatically promoted Kruger United, while Milford are in third.
They will face the side that finishes 15th in the Betway Premiership for a place in the topflight next season, with those games to be played between May 26 and June 13.
City will be hoping for a quick return to the topflight, while Milford have never been there before.
City will host Milford in the first game of the play-offs, before travelling to the 15th placed side in the Betway Premiership on May 30.
They will conclude with Milford at the side that finishes second last in the Betway Premiership.
City and Milford have played twice this season, with the KwaZulu-Natal side winning 1-0 at home and a 2-2 draw in Cape Town.
Baroka FC and Black Leopards were already confirmed as relegated before the final round of matches on Sunday.
Promotion Play-off fixtures
May 26: Cape Town City vs Milford FC
May 30: 15th Betway Premiership vs Cape Town City
June 3: Milford vs 15th Betway Premiership
June 6: Milford vs Cape Town City
June 10: Cape Town City vs 15th Betway Premiership
June 13: 15th Betway Premiership vs Milford