Some spectators at the Second Test at Port Elizabeth were spotted wearing masks depicting Sonny Bill Williams, who was involved in a much-publicised encounter with Warner's now wife Candice in 2007.
Cricket commentators and fans have slammed with stunt with The Australian cricket writer Peter Lalor calling the incident a "disgraceful new low".
Clive Eksteen, a former left-arm spinner and CSA's head of commercial, and Altaaf Kazi, CSA's head of media and communication, are the men in question.
The South African board, however, released a statement on Saturday apologising to CA and the Australian cricket team.
Warner has been embroiled in a sledging battle throughout the Test series, particularly with South Africa wicketkeeper Quinton de Kock.
"While CSA respects the rights of its fans to represent their own points of view, CSA does not associate itself with these actions and urges all Protea supporters from refraining from being involved in distasteful or unwelcome actions that may impact the image of the sport and its supporters".
According to the Sydney Morning Herald, the Australian team were "outraged" by a decision to allow the masks to be brought into the ground.
CSA said Eksteen and Kazi were now subject to "internal processes".
"On behalf of CSA I extend my honest apologies to the Board of Cricket Australia (CA), its officials, team management, players and their families", commented CSA President Chris Nenzani.
The allegations are the latest development in what has been a fractious series. Warner had delivered a stream of verbal abuse towards de Kock as the players walked off the field, but did not take well to de Kock's reply.
That incident came to light after security camera footage of the players making their way back to the dressing rooms inside the stadium was leaked to the media.
Umpires have repeatedly pulled up both Australia and the Proteas about their sloppy bounce returns, while Warner was fined in 2014 after accusing AB de Villiers of using his keeping glove to wipe the rough side of the ball. Australia's Nathan Lyon also was punished for an over-zealous celebration of a wicket in that first test.
Eksteen and Kazi are under investigation for associating themselves with the unsavoury attempt to embarrass Warner and wife Candice, who had attended day one at St George's Park with the couple's two children.