The decision was confirmed by the South African Football Association (SAFA) after Madagascar requested that supporters be excluded from the opening match of the two-legged qualifying tie.
Madagascar listed as home team
Although the first leg will take place at the Free State Stadium in Bloemfontein, Madagascar are officially the designated home team for the fixture.
The island nation does not have a suitable venue for the encounter, resulting in the match being staged in South Africa. Madagascar subsequently requested that the game be played without spectators.
SAFA confirmed that the request means no fans will be admitted for Friday's match.
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First leg set for Friday
The opening match is scheduled for Friday, 9 October, at the Free State Stadium.
CAF lists the fixture as a second-round Olympic qualifier, with the first leg scheduled for 16:00 GMT, while South African reports have the kick-off at 15:00 South African time.
South Africa's Banyana Banyana have already begun preparations in Bloemfontein under head coach Desiree Ellis, with the team determined to secure a strong result despite the unusual atmosphere created by the closed-door arrangement.
Ellis has warned her players against underestimating Madagascar, insisting that FIFA rankings will have no bearing on what happens on the pitch.
Supporters allowed for return leg
While fans will miss the first encounter, supporters will be allowed into the stadium for the return fixture.
The second leg will also be played at the Free State Stadium on Tuesday, 13 October, with kick-off scheduled for 18:00 local time.
The two matches will determine which nation progresses to the third round of the African qualifying tournament on the road to the Los Angeles 2028 Olympic Games.
South Africa are seeking a return to the Olympics after missing the Tokyo 2020 and Paris 2024 Games, while Madagascar advanced to the second round after eliminating South Sudan 2-1 on aggregate in the opening round.
Banyana targeting a strong advantage
With the first leg being played on South African soil despite Madagascar's home designation, Banyana Banyana will be expected to take advantage of their familiarity with the venue.
Ellis has stressed the importance of establishing control early in the tie, while also warning her players that Madagascar cannot be taken lightly.
The winner over the two legs will advance to the next stage of the lengthy African qualification process for Los Angeles 2028. CAF's qualifying schedule has the third round set for February and March 2027, with the final two African Olympic places to be decided in the fifth and final round later in 2027.