The suspect, 25-year-old Zenokuhle Mbatha, will be held in custody until his next court appearance on Nov. 11, South African police said.
Police said Mbatha was placed in a lineup and "positively identified" by witnesses to the killing of Meyiwa, who was shot in the upper body during an apparent house robbery on Sunday night while visiting his girlfriend.
The suspect also faces a charge of armed robbery, said Nathi Mncube, spokesman for the National Prosecuting Authority.
Police said they are hunting two more suspects and investigations are at a "very sensitive stage."
Meyiwa, a goalkeeper for South Africa and club team Orlando Pirates, was fatally shot in the township of Vosloorus near Johannesburg. The death of the popular player and national team captain led to an outpouring of dismay and anger in South Africa, which has a high murder rate.
Authorities said three suspects were involved in the break-in that led to Meyiwa's death. Police launched a manhunt and offered a reward of nearly $23,000 for information leading to the arrest and conviction of 27-year-old Meyiwa's 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 finalize the investigation and ensure that we can link all suspects to the murder," police said in a statement.
South African officials on Thursday called for a strict new gun law as a tribute to Meyiwa. The calls were made at a memorial service to honour Meyiwa and two other South African sports figures, who all died in the space of a few days.
Former 800-meter world champion runner and Olympic silver medallist Mbulaeni Mulaudzi was killed in a car crash on Friday, and female boxer Phindile Mwelase died Saturday after being in a coma following a bout.
All three will be buried in their hometowns over the weekend.
AP Sports Writer Gerald Imray contributed to this report from Stellenbosch, South Africa.