Set a target of 135, the home team were quickly in trouble at 64-4 in the 11th over with Proteas seamers Nandre Burger and Gerald Coetzee doing the damage in front of a capacity crowd.
Namibia captain Gerhard Erasmus played a vital knock to resurrect the innings with a run-a-ball 21 before Zane Green (30 not out) and Ruben Trumpelmann (11 not out) saw them over the line to wild celebrations.
The Proteas had earlier reached a total of 134-8 in their 20 overs with most of the batters struggling to adapt to what seemed a slow pitch.
Jason Smith top-scored with 31 from 30 balls while Rubin Hermann struck 23 and Lhuan-dre Pretorius 22.
Quinton de Kock failed on his return to international cricket after being didmissed with the last ball in the first over of the match for a single.
A big concern for the Proteas will be an injury suffered by fast bowler Coetzee, who limped off the field after bowling nine balls with a pectoral muscle injury.
The paceman will return home for scans and is now a major doubt for the upcoming white-ball matches in Pakistan.
The Proteas start a two-match Test against Pakistan in Lahore on Sunday that will be followed by three T20Is and three ODIs.
Tony de Zorzi was standing firm on 81 not out but the Proteas suffered a batting collapse to hand Pakistan the advantage at stumps on the second day of the first Test in Lahore.
The Proteas struck early, but Pakistan ended Day 1 of the first Test on a commanding 313/5 in Lahore on Sunday.
Kyle Verreynne says the Proteas will take inspiration from a successful tour to Bangladesh last year ahead of the Test series against Pakistan that starts in Lahore on Sunday.
The Proteas are preparing for extreme spin-friendly pitches in the upcoming Test series in Pakistan, with stand-in captain Aiden Markram saying they have "all bases covered" for conditions.
