The International Rugby Board have charged South Africa with misconduct for wearing armbands in protest of the suspension of Bakkies Botha.
The Springboks wore white armbands with the words "Justice 4 Bakkies" written on them during Sundays third Test against the Lions.
Botha was given a two-week ban for a dangerous charge on Wales prop Adam Jones seven days earlier, sparking the protest orchestrated by captain John Smit and the South African Players' Association.
But the IRB have reacted by claiming the South Africa Rugby Union are in breach of "regulations relating to the game, including breaches of the IRB code of conduct".
A statement read: "The IRB takes the view that such an act demonstrates a clear disregard for the disciplinary process.
"It 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 not binding as he cleared Jones from a ruck, an incident which left the Lions front row with a dislocated shoulder and out of the game for six months.
The Springboks launched an unsuccessful appeal and then called for rugby's judicial system to show "greater consistency" in the application of the law.