Substitute Kris Boyd scored the only goal of the game to give Scotland an unlikely victory at Pittodrie.
South Africa dominated the first half but failed to capitalise and fashion a lead despite penning the Scots in for most of the opening period.
Scotland improved after the break and Boyd scored with a half-volley after 71 minutes following a superb ball from captain Darren Fletcher.
The visitors could not find an equaliser as the Scots held on.
Scotland struggled to create many goalscoring opportunities in a first half which the visitors looked the more likely to break the deadlock.
On the half-hour mark, the unmarked Nomvethe missed the best chance of the half when he headed a Carnell cross over the bar from 16 yards.
Moments later Nomvethe flashed in a cross-shot which Scotland goalkeeper Craig Gordon did well to palm away from danger.
McFadden fired a free-kick from 25 yards over the bar after 37 minutes as the Scots failed to test the South African goalkeeper.
Bafana Bafana substitute Siyabonga Nomvethe, on for Sibusiso Zuma, who missed the best chance of the match when he headed a Bradley Carnell cross over the bar.
Scotland looked sharper after the break and substitute Kris Boyd gave the home side the lead after 71 minutes.
Fletcher played a ball over the top of the South African defence and Boyd timed his run to perfection before hitting a crisp half-volley into the net.
Barry Robson cleared Thembinkosi Fanteni's header off the line to preserve Scotland's slender lead as the visitors failed to restore parity.
Scotland: Gordon, Hutton, Anderson, McManus, McEveley, Brown, Caldwell, Fletcher, McFadden, O'Connor, Miller. Subs: Neil Alexander, Graham Alexander, Berra, Pearson, Robson, Teale, Beattie, Boyd, Maloney, Marshall.
South Africa: Fernandez, Nzama, Mokoena, Mhlongo, Carnell, Pienaar, Zothwane, Sibaya, Buckley, Nkosi, Zuma. Subs: Marlin, Mere, Fransman, Evans, Modise, Vilakazi, Nomvethe, Dikgacoi, Sheppard, Fanteni.
Referee: Martin Atkinson
~RS~q~RS~~RS~z~RS~34~RS~)