Namibia batted first and posted 163 for nine in their 20 overs, before restricting the visitors to 145 for nine in reply.
The result makes it two wins from two for Namibia against their neighbours having won the first T20 clash between the sides last October, also in Windhoek.
Namibia’s innings was anchored by a superb 60 from 38 balls by Jan Frylinck, who put on an opening stand of 84 with Louren Steenkamp (41 from 29 balls).
At one stage 200 looked on for the home side, but they managed only 40 runs from the final 35 balls of the innings as South Africa bowled well at the death.
Spinners Bjorn Fortuin (2-17) and Prenelan Subrayen (3-32) were the pick of South Africa's bowlers.
South Africa struggled from the start of their reply and when Brevis fell for a well-played 75 from 50 balls, which included five sixes, their chances of winning the game diminished.
South Africa, who have rested the majority of their regular players, meet Zimbabwe in the second Tri-Series fixture at the same venue on Saturday.