The man was arrested on Tuesday after an intelligence-driven operation, according to police spokesperson Capt Kay Makhubele.
He said a search for a second person suspected of being involved in the crime was under way.
Sibeko, of Jabulani, Soweto, was reported missing last Thursday after she failed to return home from a local spaza shop.
The teen’s partially decomposed body was later found buried in a shallow grave near a river stream in Emndeni, several kilometres away from her home. She had been raped.
Sibeko’s aunt, Bongekile Phakathi, said the 22-year-old suspect was not known to the family, and expressed relief at the arrest.
“We can’t say we’re happy, but the news about the arrest comes as a relief to the family. We hope justice will be served,” she told reporters
Gauteng education MEC Panyaza Lesufi, who visited the family on Monday, called on authorities to leave no stone unturned in apprehending those responsible for the crime.
“We can’t have a person murdered like this and be business as usual. We need to hunt the killers and provide the family with answers,” he said at the family home on Monday.
Phakathi confirmed Sibeko would be laid to rest on Thursday.