Last week FIFA opened proceedings against the English and Polish FAs after Poland fans lit flares at their World Cup qualifier at Wembley on the same evening.
Croatian fans launched flares and set off smoke bombs during the Group A match which Scotland won 2-0.
Although the Croatian were responsible for setting off the devices, the Scottish FA is facing FIFA sanctions because it was responsible for stadium security.
"We can confirm disciplinary proceedings have been opened against the SFA and the Croatian Football Federation for incidents reported during the preliminary competition match of the 2014 FIFA World Cup Brazil between Scotland and Croatia on October 15," FIFA said in a statement.
"As the proceedings are ongoing we cannot comment further."