South Africa head coach Rassie Erasmus said replacement lock forward Eben Etzebeth deserved his late red card for gouging Alex Mann.
The world champions ran riot with 11 tries as Wales sunk to a new low at Principality Stadium.
However, there was a sour ending for South Africa as Etzebeth was sent off in the final minute.
Erasmus said: "I don't know what I can say that isn't controversial. It didn't look good.
"It was a justified red card. It's definitely not the way we'd have liked to have ended the game. The optics weren't great."
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Erasmus offered future hope for Wales, having played in South Africa's record 96-13 win against them at Pretoria in June 1998 only to be on a losing Springboks side in Cardiff 12 months later.
"I refer to '98 and '99 because it shows things can change quickly," Erasmus said.
"You've got the support here and if you can get on a little bit of a roll, things will change."