The German has ten days to respond to the charge or he could face a touchline ban for his actions, though the 63-year-old has since apologised for the incident
The former Bayern Munich trainer was unhappy with the performance of the referee in his team's 1-1 draw and targeted his opposite number – an action than has landed him in hot water with the game's governing body.
"The Deputy Chairman of the Fifa Disciplinary Committee Rafael Esquivel decided yesterday to open disciplinary proceedings against Ottmar Hitzfeld," read the Fifa website.
The 63-year-old now has ten days to respond to the action, though he admitted to the Swiss press after the match that he had let his emotions get the better of him.
"I'm sorry for the gesture. I was just p****d off at not being able to take home three points," he told Blick.
"It's always difficult to play against twelve men [in direct reference to Spanish referee David Fernandez Borbalan]."
Hitzfeld takes his side to Iceland on Tuesday evening as they look to stretch their lead at the top of Group E.