Provincial police said in a statement that the owner, aged 52, was arrested over the weekend, while two employees at the tavern were subsequently arrested on Tuesday.
The owner is expected to appear before the East London Magistrates Court on Aug. 19 to face charges after an investigation that focused on allegedly supplying minors with alcohol, the statement said.
"Just as we said in the beginning, investigation is a process and needs to be treated with extreme care," Lieutenant-General Nomthetheleli Mene said in the statement.
Forensic teams are yet to reveal their conclusions on how the teens died, with a source close to the investigation saying one theory was a chemical or gas leak and authorities also investigating possible accidental poisoning.
There has been an outpouring of grief at the deaths at the nightspot in Scenery Park township, in a nation used to seeing casualties from a pervasive binge drinking culture.
Angry mourners of some victims have complained that weeks of calls to shut down the tavern went unheeded.