The South Africa Rugby Union were charged on Monday by the sport's governing body the International Rugby Board for alleged misconduct in breach of the IRB Regulations Relating to the Game including breaches of the IRB Code of Conduct.
The IRB pressed the charges because the Springboks wore armbands during the Third Test defeat to the British and Irish Lions on Saturday as a symbol of solidarity for Bakkies Botha.
The protest came following the upholding of his two-week suspension by an independent Appeal Committee for dangerously charging into a ruck without binding on a player.
The IRB takes the view that such an act demonstrates a clear disregard of the disciplinary process and does so in a manner which brings, or has the potential to bring, the Game into disrepute.
The IRB has notified the South Africa Rugby Union that it intends to begin the disciplinary proceedings.
The matter will now be referred to the independent Judicial Panel Chairman who will appoint a Judicial Officer or Committee.
Botha was banned for two weeks for the second-half charge in the Springboks nailbiting second Test victory over the Lions - which gave them the series - on Adam Jones that left the Welsh prop needing corrective surgery to right a dislocated shoulder.
The Springbok and Lions coaching staff, as well as Jones, have insisted that they saw nothing untoward in the second-rower's charge, arguing he had merely been clearing a ruck.
"As a sign of solidarity the Springbok players decided to wear white arm bands during the Test match," said Piet Heymans, head of the South African Rugby Players Association (SARPA).
"At the same time the players want to send a clear message that they require the IRB to have an urgent and serious relook at Law 10.4 (j)."