The West Ham United midfielder, on loan from Barcelona, ostensibly agreed to end his boycott in the wake of his fractious relationship with Samuel Eto'o and others during the 2014 World Cup in Brazil.
Song, 28, was named in Hugo Broos' squad after discussions in London with the new coach, but he has since told the Belgian he is not going to play against Bafana Bafana on Saturday in Limbe and in Durban on Tuesday.
He has a long history of niggling injuries to add to his disdain with Cameroon.
Georges Mandjeck, from French second division side Metz, has been called up in Song's place.
Choupo-Moting, who plays for Bundesliga giants Schalke 04, pulled out with injury.
Also out is Montreal Impact's Ambroise Oyongo.
His replacement is Abouna Ntsana, who played for AC Leopards in Dolisie against Mamelodi Sundowns on Saturday in the African Champions League.
Cameroon began their training for the match against South Africa on Monday.
source: Times Live