The 27-year-old had left his South African franchise the Lions around the 43rd over on Sunday before heading straight to the airport, having signed for Worcestershire in the English County season.
Swanepoel will now miss the opening rounds and face disciplinary proceedings in South Africa, with CSA charging him with bringing the game into disrepute.
He will face two separate disciplinary actions - one from CSA and another from the Lions - and will not contest the charges, according to the report.
"The incident was formally reported by the Match Referee and has been referred to Cricket South Africa’s disciplinary and governance structures for consideration in line with CSA regulations and the applicable Code of Conduct," CSA said in a statement on Thursday.
"CSA stresses that no assumptions or conclusions will be made prior to the completion of this process.
"Cricket South Africa reaffirms that strict adherence to playing conditions, operational protocols, and professional communication standards is non‑negotiable, particularly in showpiece fixtures such as domestic finals. "
If an agreement cannot be reached between Swanepoel and the involved parties, he may be required to drop his NOC entirely and return from England to continue his domestic career in South Africa.
Alternatively, should he choose to remain abroad, he would not need an NOC, though that might end his prospects at domestic level in the country.
"Beyers would probably say he's made a bit of an error in hindsight," Worcestershire director of cricket Ashley Giles told BBC Hereford and Worcester on Tuesday.
"I can say there was no pressure on our side on Beyers' arrival in the country at that time, or taking those steps.
"People make mistakes. Beyers is a good man, a good lad. He's made an error in this case and we're trying to work our way through it."
Worcestershire, who were relegated to Division Two of the County Championship last season, open their campaign against Derbyshire on Friday.
