Naismith faces a potential three-match ban over his alleged elbow on Serbia's Srdan Mijailovic during the 0-0 draw on September 8.
A FIFA statement read: "We can confirm that FIFA has now opened disciplinary proceedings against the player Steven Naismith."
It went on: "The case will be on the agenda for the FIFA Disciplinary Committee on October 5. "However, before then, the SFA have until the end of this week (Friday September 28) to provide FIFA with their position regarding the case."
Television pictures showed the Everton player raising his arm towards Mijailovic in the goalless World Cup qualifier at Hampden on September 8.
The incident was not included in the referee or match delegate's report but FIFA have since launched an inquiry after being made aware of the flashpoint.
Scotland face Wales on October 12 in Cardiff before facing Belgium in Brussels four days later and are in need of points to boost their qualifying hopes after drawing home games against the Serbs and Macedonia.
Naismith, 26, could also miss the away game against Serbia in March if given the maximum ban.