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Hogg is now his country’s joint-top all-time try scorer, with 24 to his name, but he could not mark the occasion with a victory.
South Africa, who had director of rugby Rassie Erasmus reprise his controversial role as water carrier, starved Scotland of the ball in the first 15 minutes but could not covert their time in the home side’s 22 into points.
The teams traded penalties before the visitors hit the front as they fed off some scrappy Scotland play with ball in hand.
Centre Lukhanyo Am won the turnover and, as the ball went wide, the electric Makazole Mapimpi raced down the touchline to score a try.
Scotland hit back off some poor ball retention from the visitors and showed good hands down the left wing as Hogg went over for a converted score that gave his side a 10-8 half-time lead.
But South Africa turned it up a notch in the second half with fresh forward power off the bench that Scotland simply could not counter.
They hit the front again three minutes into the second period when Am won another turnover and centre Damian de Allende broke between two defenders before feeding Mapimpi to score his second try.
Jantjies extended the lead to 11 points with two penalties, but the hosts stayed in the contest with a second try for Hogg after an excellent move from an attacking line-out.
At that stage they trailed by six points, but the Scots missed three more attacking lineouts in quick succession on their own throw in a momentum-killer for them.
The visitors finished much the stronger in the final 15 minutes and took full advantage of the penalties presented to them. South Africa now turn their attention to next weekend, when they will face England at Twickenham.
Additional reporting by Reuters