Both and team mate Schalk Burger were both cited for incidents during the 28-25 second Test victory by the world champions. Botha was banned for two weeks for an incident at a ruck that left the Lions prop with a dislocated shoulder, while Burger was given an eight week ban for eye gouging.
The Springbok coaching team were incensed at the action taken against Bulls lock Botha and are determined to overturn his suspension at an appeal hearing later this week.
"Bakkies was very upset about the citing because he has worked so hard to ensure he is very accurate in those situations. He is a really powerful man and he is very good at those clear outs at rucks," said South African assistant coach Dick Muir.
"He does the dirty work and that's the reason he is in our side. We possibly feel that there is an element of his reputation going before him.
"The IRB produced a film of what is right and wrong at cleaning out at the rucks and they used Bakkies as an example in that. Perhaps this is where it has come from.
"We don't see any wrong doing in that challenge. If it wasn't for the injury I don't think anything would have been done about it.
"It is a major concern for us and there were other tougher incidents that could possibly have been citings in the game. It is a bit of a disruption from a selection point of view so it causes a bit of disarray to our preparations.
"We realise that it is a tough game. Bu what was disappointing for us was there was no reason for Bakkies to be cited.
"We are concerned what the game is coming to. If you aren't able to clear out at the rucks, which is a big part of the game, we feel it could change the face of the game."
Springboks forwards coach Gary Gold described Botha's work at the ruck four minutes into the second half that left Jones with his injury as a "text book clean out".
"His body position was fantastic and he arrived with the intention of staying on his feet," said Gold.
There will be no appeal against the Burger ban, but the move on Botha's punishment will mean another hearing over the next three days which could clear him to play against the Lions on Saturday.
Gold also believes that having an Australian referee will benefit the game and both teams. The Springboks know Stu Dickinson very well from international and Super 14 rugby and believe he will be a better communicator than Frenchman Christophe Berdos was last weekend.
"Both teams will be particularly relieved that there is a referee whose interpretations we will understand better. From a communication point of view it will be easier - it will be a better day for both teams," added Gold.