The match at the San Siro was temporarily stopped in both halves by Dutch referee Bjorn Kuipers after visiting fans threw fireworks and smoke bombs on the pitch.
Charges of racist behaviour, crowd disturbances and the setting-off of fireworks and missiles have been levelled against the Croatian Football Federation.
The Italian Football Federation has been charged as a result of the setting off of the fireworks.
The case will be dealt with by UEFA's Control, Ethics and Disciplinary Body on December 11.
The match finished 1-1 after Antonio Candreva put the hosts ahead in the 11th minute only for Ivan Perisic to equalise four minutes later.
The result left the two sides level on 10 points at the top of Group H after four games, with both teams having gone into the encounter on the back of three straight wins.