Lote Tuquri and Stirling Mortlock were the try scorers for the hosts, with a long-range drop goal from Berrick Barnes sealing victory in the final minute of play.
Lions head coach Ian McGeechan will have taken note the nine turnovers conceded by the Boks at ruck and maul situations as they finished the away leg of this year's Tri Nations with a total of five points from a possible 15.
South Africa will now enjoy a three-week break before playing taking on Argentina on August 9, followed by their final three Tri Nations fixtures in successive weeks.
South Africa's remaining fixtures in the 2008 Tri Nations:
August 16 New Zealand, Cape Town
August 23 Australia, Durban
August 30 Australia, Johannesburg
South Africa's confirmed remaining fixtures in 2008:
November 8 Wales, Millennium Stadium
November 15 Scotland, Murrayfield
November 22 England, Twickenham