Saint-Andre has dropped four other players from his preliminary squad, axing Sébastien Vahaamahina, Xavier Chiocci, Loann Goujon and Remi Lamerat.
Lamerat of Castres was dropped in favour of Toulouse centre Gaël Fickou and, while the front trio of Vahaamahina, Chiocci and Goujon were not expected to make the cut, Trinh-Duc's absence comes as a surprise.
"[It was a] difficult moment to see the five players leave the group," Saint-Andre said in a statement.
Trinh-Duc is a casualty of the resurgence of Michalak, who became France's all-time record points scorer during the 25-20 victory over England in Paris at the weekend.
Another rival for the flyhalf role was Rémi Talès, whose importance to the squad as an off-field leader is also a reason why Trinh-Duc has missed out.
France welcome Scotland to the Stade de France on September 5 in another pre-tournament warm-up match, before they begin their World Cup campaign against Italy at Twickenham on September 19.
France squad:
Forwards: Uini Atonio, Eddy Ben Arous, Vincent Debaty, Nicolas Mas, Rabah Slimani, Guilhem Guirado, Benjamin Kayser, Dimitri Szarzewski, Alexandre Flanquart, Yohann Maestri, Pascal Papé, Thierry Dusautoir, Bernard Le Roux, Yannick Nyanga, Fulgence Ouedraogo, Damien Chouly, Louis Picamoles.
Backs: Rory Kockott, Morgan Parra, Sébastien Tillous-Borde, Frédéric Michalak, Rémi Talès, Mathieu Bastareaud, Alexandre Dumoulin, Gaël Fickou, Wesley Fofana, Sofiane Guitoune, Yoann Huget, Noa Nakaitaci, Brice Dulin, Scott Spedding.
