Meyiwa, 27, was killed on October 26 following an alleged altercation involving two attackers at a property in Vosloorus on the outskirts of Johannesburg.
The South African Police Service subsequently confirmed that Zanokuhle Mbatha, 25, had been arrested and charged in connection with the death, with the accused due to appear in court on Tuesday.
However, the magistrate at the court in Boksburg revealed that the charges had been withdrawn.
"From the submissions made by prosecutor Getrude Market the court has accepted that as of now there is not sufficient evidence to put Mr Mbatha to trial," Daniel Thulare is quoted as telling the court by the South African Press Association.
"I note the withdrawal of charges by the State against Mbatha and consequently the court orders the release of Mr Mbatha today."
Speaking on the steps of the court following the ruling, National Prosecuting Authority spokesperson Nathi Mncube said: "There was a lot of discrepancies, inconsistencies, and a lot of contradiction in the evidence that we felt we could not continue with the matter.
"Our view is that there is no prospect of a successful prosecution and we thought it would be fair to withdraw the matter and allow the police to investigate."
The investigation continues.
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