Play had to be held up for five minutes as police and stewards moved in to stop visiting fans from trying to gain access to the Park End stand while seats and other projectiles were thrown onto the pitch and towards the home end.
European football's governing body says they will censure the Croatian club Hajduk for "throwing of objects", "crowd disturbances", "field invasions by supporters" and "acts of damages" while Everton will be charged with the "throwing of objects".
A Hajduk fan site says that the actions of the travelling Croatians were in response to coins being thrown at them, however an account from an Evertonian close to the incident claims that the coin-throwing started from the away section.
Additionally, Blues supporters in the Paddock next to the away section have remarked on how many opposition "fans" had come dressed in hooded sweaters, sunglasses and scarves over their faces, the common attire of "ultras" who are often blamed for inciting crowd disturbances at games on the Continent.
The date of the hearing has not been set but the incident will heighten the need for security during the second leg next Thursday when an unknown number of Evertonians will travel to Split to support their team.