A try by hooker Adriaan Strauss and three penalties from flyhalf Patrick Lambie gave the South Africans a 14-3 lead at the break.
A sole penalty from No 10 Greig Laidlaw was the only score for the home side.
Scorers:
Scotland:
Penalty: Greig Laidlaw
South Africa:
Try: Adriaan Strauss
Penalties: Patrick Lambie (3)
Teams:
Scotland:
15 Stuart Hogg, 14 Sean Lamont, 13 Nick de Luca, 12 Matt Scott, 11 Tim Visser, 10 Greig Laidlaw, 9 Mike Blair, 8 David Denton, 7 John Barclay, 6 Kelly Brown (captain), 5 Jim Hamilton, 4 Richie Gray, 3 Euan Murray, 2 Ross Ford, 1 Ryan Grant
Substitutes: 16-Dougie Hall, 17-Kyle Traynor, 18-Geoff Cross, 19-Alastair Kellock, 20-Stuart McInally, 21-Henry Pyrgos, 22-Ruaridh Jackson, 23-Peter Murchie
South Africa:15 Zane Kirchner, 14 JP Pietersen, 13 Juan de Jongh, 12 Jean de Villiers (captain), 11 Francois Hougaard, 10 Pat Lambie, 9 Ruan Pienaar, 8 Duane Vermeulen, 7 Willem Alberts, 6 Francois Louw, 5 Juandré Kruger, 4 Eben Etzebeth, 3 Jannie du Plessis, 2 Adriaan Strauss, 1 Gurthrö Steenkamp
Substitutes: 16. Schalk Brits, 17 Heinke van der Merwe, 18 CJ van der Linde, 19 Flip van der Merwe, 20 Marcell Coetzee, 21 Morné Steyn, 22 Jaco Taute, 23 Lwazi Mvovo
Referee: George Clancy (IRL)