The Springboks - without the experience of Jean de Villiers or Victor Matfield - called on a youthful backline and Handre Pollard, who was given the nod at stand-off ahead of Pat Lambie, marshaled them expertly.
And, despite a superb second-half try taking Scotland to within touching distance of the two-time world champions, Pollard's boot and a Bryan Habana try put the result beyond doubt.
The win moves South Africa top of the pool, just one point better off than Scotland who are in turn two ahead of the impressive Japanese.
Defeat to Japan in the opening round may have taken some of the fear factor from South Africa and Scotland began in confident fashion, running the ball out of defence and kicking a penalty inside the Springbok half to touch.
However, it was Heyneke Meyer's side who went ahead on 12 minutes, pummeling their way past a resilient Scottish wall for Burger and Bismarck Du Plessis to pile over together, the former eventually grounding the ball.
Confirmation from the TMO allowed Pollard to convert and the young fly-half added three more points from the tee five minutes later when the Scots were pinged at the maul.
South Africa reached the 25-minute mark still yet to concede a point and Pollard soon had three more at the other end, tapping over after Fraser Brown was caught offside.
Those Scottish points did arrive, however, on the half-hour mark, when Greig Laidlaw fired a long-range penalty just inside the left-hand upright.
Still, it was the Springboks who threatened and, two minutes before the break, Scotland - their tackle count nearing 100 already - were breached again.
Captain Fourie Du Preez profited from a dominant lineout drive to feed Pietersen - hat-trick hero against Samoa last weekend - to score, Pollard converting.
Scotland emerged after the break with a 17-point gap to breach and Laidlaw took an early slice out of that from the tee. Then, in some style, they got even closer.
Duncan Weir intercepted a pass on his own try line before streaking all the way to the Springbok 22 and spectacularly offloading to Tim Visser in the tackle.
He found Tommy Seymour, who crossed over, and Laidlaw added the extras, though a Pollard drop-goal two minutes later opened the gap back up to ten.
Laidlaw was soon in the sin bin himself, for tackling Habana off the ball, and Weir - taking over the kicking duties - made slotted his first penalty on the hour.
But indiscipline began to cost Scotland and, after a pair of quickfire Pollard penalties made it 29-16 with just 12 minutes left, Habana put his side out of reach.
The 32-year-old, collected a Du Preez pass, brushed off a tackle and reached out for the line to put the finishing touch on proceedings.