The visitors, who had spent almost five sessions in the field as Australia A amassed 480 for seven, batted out the first two sessions of the third and final day before declaring on 277 for six, 203 runs behind.
The hosts were expected to face 27 overs from the world's best pace attack in the final session, but both captains decided to end the match at the Sydney Cricket Ground an hour early with Australia A on 13 for one.
After their bowlers toiled for much of the first two days, South Africa's batsmen were given every opportunity to get accustomed to Australian conditions with both Hashim Amla (53) and captain Graeme Smith (60) opting to retire shortly after they reached their half centuries.
The middle order duly obliged with JP Duminy (31) and Jacques Rudolph (39) both crafting patient innings on the slow-paced pitch, while AB de Villiers and Faf du Plessis both scored 24 runs before Smith decided the bowlers needed another workout and declared their innings closed at the tea break.
The visitors, who are the world's top-ranked Test side, head into the first Test at the Gabba in Brisbane on November 9 with few injury concerns, though De Villiers is nursing minor ankle and back injuries.