Gourcuff picked up a thigh injury in Bordeaux's 1-0 home win over Maccabi Haifa in the Champions League on Wednesday.
"(Assistant coach) Alain Boghossian was at the game yesterday and he talked to Yoann. He observed that he would not be fit for these two matches," Domenech told reporters.
Former captain Patrick Vieira, who has been plagued by injuries recently and has not played for France since last year, was also ruled out because of a lack of match fitness.
"I talked to him over the phone. We agreed that he must play more, he knows that," said Domenech, who picked four goalkeepers to make up for Hugo Lloris's suspension against the Faroe Islands on October 10. The Lyon keeper was sent off in a 1-1 draw in Serbia last month.
France host Austria four days later in a bid to snatch at least a playoff spot for next year's World Cup finals.
Les Bleus lie second in European qualifying Group Seven, four points adrift of Serbia.
Goalkeepers: Steve Mandanda (Olympique Marseille), Hugo Lloris (Olympique Lyon), Cedric Carasso (Girondins Bordeaux), Nicolas Douchez (Stade Rennes)
Defenders: Eric Abidal (Barcelona), Patrice Evra (Manchester United), William Gallas (Arsenal), Julien Escude (Sevilla), Gael Clichy (Arsenal), Rod Fanni (Stade Rennes), Sebastien Squillaci (Sevilla), Bacary Sagna (Arsenal)
Midfielders: Alou Diarra (Girondins Bordeaux), Abou Diaby (Arsenal), Jeremy Toulalan (Olympique Lyon), Florent Malouda (Chelsea), Lassana Diarra (Real Madrid), Moussa Sissoko (Toulouse)
Forwards: Karim Benzema (Real Madrid), Thierry Henry (Barcelona), Franck Ribery (Bayern Munich), Andre-Pierre Gignac (Toulouse), Nicolas Anelka (Chelsea), Sidney Govou (Olympique Lyon)
