Motjeka Madisha of Mamelodi Sundowns has been called up to replace Mathoho.
The towering defender was part of the 25-man squad called up by Bafana Bafana head coach Stuart Baxter, pending a decision from the FIFA Disciplinary Committee (FDC), which sat on Friday to deliberate on the match ban.
According to a communiqué from FIFA: “Erick Mathoho is regarded as having breached art. 48 par. 1 c) of the Fifa Disciplinary Code by committing an act of unsporting conduct against an opponent in the scope of the match played between the representative teams Cape Verde Islands and South Africa on September 1.
Mathoho is suspended for two matches including the automatic match suspension, which was served in the match played between the representative teams of South Africa and Cape Verde Islands on September 5.
“The following match suspension has to be served during the match to be played between the representative teams of South Africa and Burkina Faso, scheduled on October 7.”
Mathoho has once again apologised to the nation for the incident.
“Words fail me when I think of the incident and the red card itself, but from the bottom of my heart I want to once again apologise for my actions – to the entire Bafana Bafana team and all the football-loving fans,” said Mathoho.
“Let me also take this opportunity to wish the team all the best against Burkina Faso in this crucial match. I know it’s not going to be easy but I have confidence that they will get positive results. We did not do well in the last two matches but I believe we will rise again, starting with this upcoming clash. Good luck to all.”
Bafana Bafana assembled for camp on Sunday and will face the Burkinabe on Saturday at FNB Stadium (start 3pm).
South Africa played to a 1-1 draw against Burkina Faso in Ouagadougou in October last year. Dean Furman scored for Bafana Bafana.
The West Africans remain unbeaten in Group D of the 2018 FIFA World Cup qualifiers, on six points – level with Cape Verde, but Burkina Faso lead the group due to a better goal difference.
Senegal lies in third position with five points, while South Africa is bottom of the table with one point.