Leighandre “Baby Lee” Jegels was murdered in Mdantsane, in the country’s Eastern Cape at about 14:00 local time (12:00 GMT) on Friday.
Officials say the suspect was known to the 25-year-old and is a serving member of the South African Police Service.
Earlier reports indicated that the 37-year-old suspect, who was later arrested away from the scene, was the victim’s current partner.
Unnamed sources who spoke to the DispatchLive website alleged the boxer had a protection order against the man arrested.
However, a police spokesman confirmed to local media that the motive appeared to be a “domestic dispute” between “the couple”.
Jegels has not fought since August 2017 and has an unbeaten record of 9-0 with 7 knockouts.
She was expected to make her comeback in July in Saudi Arabia, however the tour was cancelled after the kingdom “revoked the move saying that women shouldn’t be involved in boxing, wrestling or any aggressive sport”.
Police have confirmed that the Independent Police Investigative Directorate (IPID) is investigating a case against the boxer’s policeman boyfriend.
(With input from BBC)