Swiss media published images of Hitzfeld making a hand gesture in the first half of a 1-1 draw with Norway in Bern on Friday.
Hitzfeld later expressed his frustration at decisions made by Spanish referee David Fernandez Borbalan.
FIFA says its disciplinary panel "will evaluate the case and define next steps."
FIFA says panel chairman Marcel Mathier, who is Swiss, has recused himself and the case will be handled by his Venezuelan deputy, Rafael Esquivel.
Switzerland leads Group E by just one point after conceding a late equalizer to Norway.
The veteran German coach takes Switzerland to face second-place Iceland on Tuesday.