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.
Proteas pace spearhead Kagiso Rabada believes some pitches at the T20 World Cup will be of assistance to the bowlers even though high scores are being predicted at the global tournament.
The Proteas fell to a 30-run defeat against India in an unofficial clash in Navi Mumbai in what was their final warm-up game ahead of the T20 World Cup that kicks off on Saturday.
Quinton de Kock praised Ryan Rickleton's ability to adjust to the No 3 role and believes the rest of the lineup will need to show similar levels of adaptability if the Proteas are to win the T20 World Cup in India.
Left-arm wrist spinner Tabraiz Shamsi says he is committed to the Proteas despite his consultancy stint with the West Indies during the recent T20 series.
