Play was suspended in the 33rd minute after supporters in the away end at Goodison Park surged towards the pitch and objects were thrown.
Everton have been charged with the "throwing of objects".
While European football's governing body have charged Croatian club Hajduk with four offences.
They are: "throwing of objects", "crowd disturbances", "field invasions by supporters" and "acts of damages".
Uefa is yet to confirm the date of the hearing.