"There was a bit of a problem between us," Deschamps said. "We've spoken about it since and I don't have a problem with what happened, and neither does he. It wasn't going to affect whether or not I picked him."
France, which plays at Georgia on Sept. 6 and at Belarus four days later, is in second place in Group I, one point behind Spain after losing 1-0 at home to the world champions in March.
Deschamps named a larger squad of 25 players because midfielders Blaise Matuidi and Paul Pogba are both suspended for the first game.
Monaco midfielder Jeremy Toulalan who also has not played since the 2010 World Cup had been expected to be recalled after some fine performances this season but was left off the squad.
"He is still very affected by what happened (in South Africa), perhaps too affected. It's up to me to take the decision," Deschamps said. "I spoke to him several times, but I won't go into details about our conversations."
Deschamps also left out midfielder Yohan Cabaye, who is usually a regular for France but is in open conflict with his club as he tries to push through a late move from Newcastle to Arsenal.
Cabaye has not played so far this season and has been absent from training.
"It's never positive for the player or for the club. These are extreme situations that unfortunately repeat themselves," Deschamps said. "Clubs have the power because they have the contracts in hand and the interests of the players don't always go in the same direction. They are free to take the right or wrong decisions and to make career choices that can obviously have consequences for the national team."
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Squad:
Goalkeepers: Hugo Lloris (Tottenham), Steve Mandanda (Marseille), Mickael Landreau (Bastia)
Defenders: Eric Abidal (Monaco), Gael Clichy (Manchester City), Mathieu Debuchy (Newcastle), Patrice Evra (Manchester United), Laurent Koscielny (Arsenal), Eliaquim Mangala (FC Porto), Adil Rami (Valencia), Bacary Sagna (Arsenal)
Midfielders : Etienne Capoue (Tottenham), Clement Grenier (Lyon), Josuha Guilavogui (Saint-Etienne), Geoffrey Kondogbia (Sevilla), Blaise Matuidi (Paris Saint-Germain), Paul Pogba (Juventus), Moussa Sissoko (Newcastle)
Forwards: Karim Benzema (Real Madrid), Andre-Pierre Gignac (Marseille), Olivier Giroud (Arsenal), Samir Nasri (Manchester City), Dimitri Payet (Marseille), Franck Ribery (Bayern Munich), Mathieu Valbuena (Marseille)