"World Rugby should have seen this coming because for years, teams – not just South Africa but France – were picking a six-two bench. It should never have been allowed to get to this.
"All World Rugby had to say was, 'Three of your bench have to be recognised backs.'
"That's all they had to do and this problem would not be there. What South Africa did the other day, I think, is totally against the spirit of the game, and certainly totally against player safety."
Williams called on World Rugby to rule before the World Cup starts.
Scotland is next in the Springboks' firing line when they open their Rugby World Cup campaigns.
But Scotland is taking a positive approach after the Springboks hammered the All Blacks 35-7 and leapt to second place on the World Rugby rankings.
Former Scotland international Richie Gray, who was part of the Springboks' coaching team at the 2015 Rugby World Cup, said the defending world champions are not unbeatable.
He said Scotland needed to do a Japan on South Africa, a reference to the 2015 win by Japan over the beaten semifinalists in that tournament.
"I remember after we were defeated by the Japanese, Eddie Jones [Japan's head coach] was talking about one-second rucks, the speed of the game and trying to keep it at a high intensity.
"Scotland have got a massive task to take on South Africa and beat them, but everybody is beatable.
"It's just going to be the game plan that Scotland go out and use, and it's going to need every one of those players being at the top of their game for that 80 minutes – and the bench," he told the BBC.
Gray is coaching with Toulon, having previously worked with Vern Cotter at Scotland, Montpellier and Fiji.
"Scotland are going to have to cope with power. The huge challenge for Scotland is how they are going to play against that. They're going to have to move South Africa around, they're going to have to have every trick in the book, to have two or three really good special plays.
"You're going to have to mix it up as much as you can and keep the pace of the game as high as you can for as long as you can."