Botha will still be available for South Africa's Tri-Nations campaign
South Africa captain John Smit fears the long-term implications for the sport after Bakkies Botha received a two-week ban for dangerous charging.
Botha was suspended after an incident which left British and Irish Lions prop Adam Jones with a dislocated shoulder.
An appeal against the ban was thrown out, but Smit believes there was nothing wrong with Botha's challenge.
"I hope it's just a case of Bakkies being victimised. If not, it could change this wonderful game," said Smit.
The Botha incident happened just after half-time of the ferocious second Test in Pretoria, with the Lions in the process of securing possession at the ruck.
Botha charged to the tackle area and collided with Jones - an incident that South Africa claim was perfectly legal "clearing out".
"If it wasn't for the injury which came from it, I don't think anything would have been said about it," said assistant coach Dick Muir.
Smit added: "Sanity did not prevail at the appeal and I've had referees phoning me, and support from the Lions management and players that it is very concerning for the future of the game.
"Unfortunately Adam Jones got injured purely because his arm was stuck in the ruck.
"If Bryan Habana is running down the wing as fast as a cheetah, it would be really poor for the game to make him slow down in case he hurts the tackler."
I sincerely hope there's no bad blood between the two teams
But despite the controversy in Pretoria - team-mate Schalk Burger is serving an eight-week ban after an eye-gouging incident - Smit expects Saturday's tour finale at Ellis Park will be played in good spirits.
"I sincerely hope there's no bad blood between the two teams," said Smit.
"Rugby's all about running into each other at a million miles an hour and tackling each other at a million miles an hour, stitching oneself up afterwards and sharing a beer.
"There is still a massive amount for us to play for because we don't get the opportunity to play against the Lions for another 12 years.
"It's been a phenomenal series, although it's probably easier for me to say that as the captain that's won."
We didn't have an issue with Bakkies Botha, it was a very tough decision on him
Lions assistant coach Warren Gatland
Lions assistant coach Warren Gatland said the tourists did not believe Botha should have been cited.
"We didn't have an issue with Bakkies Botha, it was a very tough decision on him," Gatland told a news conference on Friday.
"Adam Jones did not have an issue with the clean-out and neither did the Lions management.
"If Bakkies could be banned for that then you would have 50 incidents in a game. Bakkies has a history of occasionally not using his arms but we had no problem with that incident, we felt it was legitimate."