South Africa captain Bjorn Fortuin returned to the team, after being rested on Friday, to take 4-33 as Namibia, who elected to bat first, were dismissed for 156 runs in the 37th over.
In reply, openers Connor Esterhuizen and Jordan Hermann put on 150 for the first wicket before Hermann was bowled for 77, seven runs short of the victory.
Esterhuizen finished unbeaten on 68 while new batsman Dewald Brevis hit a six to win the game with 28.3 overs to spare.
Both Esterhuizen and Hermann had scored centuries in the first two ODIs against Namibia and kept up their form for an easy triumph.
South Africa, who rested almost all of their limited-overs regulars, were also comfortable winners in the first two ODIs of the first series between the neighbours, who, along with Zimbabwe, will co-host next year’s World Cup.