Leigh Halfpenny kicked all of the home side's points as they snapped a run of defeats at the hands of the southern hemisphere's big three stretching back over 23 games and six years.
The victory eased the pressure on coach Warren Gatland, who had been heavily criticised following Wales' late fade-outs against both Australia and New Zealand, while opposite number Heyneke Meyer was left to reflect upon a mixed tour which produced two wins and two defeats.
In a carbon-copy of last week's Test between Wales and New Zealand at the same venue, an attritional opening period yielded only a penalty apiece as the respective defences held sway.
It was the hosts who shaded it in terms of both possession and territory, but with every breakdown fiercely contested and plenty of aggressive counter-rucking on show, there was little quick, clean ball for either backline to exploit.
Halfpenny and Pat Lambie each missed respective penalty attempts after their early successes and the only other time the scoreboard even looked like moving came when Halfpenny was held up short of the line after the men in red had called two consecutive 14-man lineouts.
The narrative remained much the same during the early exchanges of the second half, with endeavour significantly outweighing inspiration, but Halfpenny did land a further two penalties to Lambie's one, moving Wales out to a 9-6 lead on 53 minutes.
And the crowd were then finally brought to their feet as the hosts earned a scrum penalty with an impressive shove that left the South African pack reeling.
Halfpenny made no mistake in stroking home the kick to ensure that his side would head into the final quarter with that drought-breaking victory within touching distance yet again.
Those prospects looked even brighter when the Springboks lost Cornal Hendricks to the sin-bin on 63 minutes, after the winger was harshly adjudged to have taken out Halfpenny in the air in what looked like an honest contest for the ball.
Seemingly determined to keep their long-suffering supporters on edge, however, Wales failed to translate their numerical advantage into any additional points and with just four minutes on the clock, found themselves defending a five-metre scrum.
Yet defend it they did and, after Willie le Roux knocked on Dan Biggar's clearing kick, Wales saw out the final seconds to secure a long-awaited victory and strike a potentially significant psychological blow against a side they may well meet at the quarter-final stage of next year's World Cup.