Springboks coach Peter de Villiers confirmed after the game he agreed with the protest, which was orchestrated by Bolks skipper John Smit and the South African Rugby Players Association (SARPA).
An IRB spokesperson told the Telegraph website: "The IRB is looking to establish all the relevant facts before making any further comment."
Smit slammed the Botha suspension as "ludicrous" and received support from the Lions management and players. His contention was that Botha was merely cleaning out at the ruck and that such a citing could set a dangerous precedent in the game.
Jones had his right shoulder dislocated in the incident and is set to be ruled out of rugby for six months when he has an operation this week.
South African Rugby Players' Association chief executive Piet Heymans explained the decision to protest.
"Over an extended period of time, numerous other players have charged into rucks without binding, but were either not penalised at all or received only a penalty," he said.
"Bakkies hit a ruck just before the one in question in a similar style and was not penalised.
"The players want to send a clear message that they require the International Rugby Board to have an urgent and serious re-look at Law 10.4.
"The inconsistency has upset the players, and they felt very strongly that they must take a firm stance and show their unhappiness with the application of the relevant law.
"We will be consulting with our legal team next week to consider all our legal options available to assist Bakkies Botha and provide him with a sense of justice."