Not even a superb score from Wales wing Shane Williams in the second half, his 42nd Test try, could gloss over Welsh deficiencies on a day when they conceded too many penalties, gifted too many turn-overs and dropped too many passes.
Butch James helped himself to 23 points as he landed nine out of nine goalkicks - five penalties and four conversions - and the fourth and final try from replacement centre Percy Montgomery took his personal points tally in eight games against Wales to 97.
It was a defeat that left Wales coach Warren Gatland rather red-faced - and will have given McGeechan plenty to think about ahead of next summer's Lions tour.
"At the end of the day we weren't good enough and we were physically dominated by a better side," said Gatland.
"We came here to earn the respect of the South Africans, but we did not get it. We are proud of what we have achieved in the last six months, but we have to be more accurate and disciplined
"Even though we were talking coming into the game about confidence and self-belief, we didn't demonstrate it.
"There is plenty to work on and we won't be throwing in the towel. In the first-half we could have been in the game because there were a few opportunities we didn't take and there were a few soft penalties."
James kicked all five penalties in the first-half, when he also converted a try from full back Conrad Jantjes. The Welsh response came via a corner try from full back Jamie Roberts and a penalty and conversion from Stephen Jones.
A turn-over at a maul six minutes after the break paved the way for a try from centre Jean de Villiers and then No 8 Pierre Spies crashed over as the world champions extended their lead to 36-10.
That Williams try temporarily improved Welsh hopes, but Montgomery, the sole Springbok survivor from the 1997 series defeat to the last Lions tour party to go to South Africa, wrapped things up with his corner score.
The two sides meet again for the Prince William Cup in Pretoria on Saturday.