Namibia had won their previous two T20 clashes with their neighbours, both against depleted South Africa teams, but this time came unstuck as the visitors posted 228 for four.
Namibia were in the contest for much of their innings but ran out of steam towards the back end as they reached 217 for three in their allotted 20 overs.
South Africa were sent in to bat and a 156-run opening stand from 69 deliveries between Pretorius and Connor Esterhuizen (88 from 40 balls) set them up for a massive total.
Both batters hit eight sixes on the flat wicket as they tore into the home bowling attack, with spinner Jan Balt (2-31 in four overs) the only one to come through relatively unscathed.
Namibia also had a fantastic start as Jan Frylinck (72 from 36 balls) and Louren Steenkamp (61 from 44 balls) put on 119 in 65 balls for the first wicket, but fell just short.
They were not helped by Steenkamp retiring hurt at the end of the 16th over after he took a blow to the head and then the arm in separate incidents.
South Africa will play Zimbabwe in the series final at the same venue on Sunday.