The police said Zanokuhle Mbatha, 25, had been charged in connection with the case. Local media said the charges included murder.
Football star Senzo Meyiwa was hit by a single gun shot to the chest on Sunday night while confronting two intruders at the home of his girlfriend, actress and singer Kelly Khumalo.
He will be buried on Saturday and his death has highlighted the phenomenon of gun violence in South Africa, coming just days after disabled track star Oscar Pistorius was jailed for shooting dead his girlfriend Reeva Steenkamp.
The National Prosecuting Authority said Mbatha had made a brief appearance in the Boksburg Magistrate court east of Johannesburg. His case was adjourned until Nov. 11.
Even though South Africa's murder rate has been gradually dropping, it remains one of the world's most violent countries, with police recording more than 17,000 murders last year, or 31 per 100,000 people - seven times the rate in the United States.
Meyiwa, 27, who also played for professional club Orlando Pirates, had legions of fans in sports-mad South Africa and police, under huge public and political pressure, have launched a massive hunt for his killers.
"Whilst we are pleased with the progress we are making and the overwhelming support from members of the public, there is still a lot of work to be done to finalise the investigation and ensure that we can link all suspects to the murder," the police statement said.
"Given the fact that our investigations are at a very sensitive stage, we will only be in a position to update the nation during a media briefing on Monday, 3 November 2014."
This weekend's Johannesburg derby between Soweto giants Kaizer Chiefs and Orlando Pirates was postponed as a mark of respect. The derby is usually played in front of 90,000 fans.
(Additional reporting by Ed Stoddard; Editing by Crispian Balmer)
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