Scotland waited 50 minutes to find their attacking game against South Africa - but some sustained pressure could not overturn an Adrian Strauss double as the visitors secured a 21-10 win.
The Scots could not cope with a first-half physical barrage and Strauss went over after a maul before intercepting Mike Blair's pass early in the second period to help open up an 18-point lead.
Replacement scrum-half Henry Pyrgos soon crossed for the home side and sparked half an hour of relentless pressure, but they missed a series of chances.
Scotland forced a series of short-range penalties but failed to take advantage through a mixture of poor decision-making, some desperate defending and crucial decisions by referee George Clancy.
Andy Robinson's side had enough chances to at least equal the three tries they scored in last weekend's 51-22 defeat by New Zealand, but they had been posted missing as an attacking force throughout the first half, although they were not helped by the loss of Richie Gray to a head injury.
Scotland head coach Robinson told BBC1 afterwards: "We've got a lot to learn. A lot to learn in improving defence and also in attack, particularly physically.
"I felt they bullied us a little in the first half."
Robinson now wants to see a reaction to the result, adding: "Next week against Tonga we need a performance there to put together the lessons they've learned from the first two games.
"There's a lot for us to look at. The disappointing thing from our side is we allowed a side to get a lead again and that's something you can't afford to do."