After stirring RBS 6 Nations Championship wins over France, England and Italy earlier this year, the Scots had high hopes of upsetting Jake White's team.
But, against a South African side packed with pace and raw power, Scotland toiled.
Tries from Schalk Burger, Breyton Paulse, Andre Snyman and Percy Montgomery sealed the triumph with the Scots stretched for lengthy periods.
Edinburgh's Simon Webster went over for Scotland's consolation try, goaled by Chris Paterson to keep his 100% record with the boot.
Glasgow's Andy Henderson was one of the few Sctland players to make any impact, while Donnie Macfadyen did well in his first international game since returning from a long time out through injury.