Noord-Kaap beat Affies 25-22 in Kimberley after leading 17-5 at the break.
The hosts scored two first-half tries through flank Christiaan de Haast and scrumhalf Zane le Roux, with Kobus du Plessis kicking both conversions. However, two tries early in the second half allowed Affies to level the scores at 17-17.
Both teams then scored unconverted tries before Van der Merwe kicked the penalty that gave Noord-Kaap the most famous victory in their 20-year rugby history.
In Gauteng, King Edward VII claimed their first away win against Pretoria Boys’ High since 1996 with a 31-15 victory.
The Joburg school, who beat Boys’ High 19-9 at home earlier in the season, scored four tries through right wing Senzo Shabalala, flyhalf Marco Engelbrecht and hooker Stephan van Rooyen, with Engelbrecht kicking two conversions and four penalties. The hosts responded with two tries from left wing Greg Colin and No 8 Kirk Pretorius. Flyhalf Rossouw de Waal slotted a conversion and penalty.
KES led 17-3 at half-time but Pretoria Boys’ fought their way back to make it 23-15 with 15 minutes to go. But a try and penalty from the visitors secured a convincing win.