Play was suspended in the 33rd minute of the match, which Everton went on to win 2-0 thanks to goals from Michael Keane and Idrissa Gueye, when objects were thrown from the away end and supporters charged towards the pitch.
The majority of the charges relate to Split's supporters, namely the throwing of objects, crowd disturbances, field invasion by supporters and acts of damage.
Everton have also been charged with the throwing of objects by their fans.
UEFA's Control, Ethics and Disciplinary Body will deal with the case, although a date for the hearing is yet to be confirmed.
The trouble began shortly after Keane headed Everton's opener and both teams waited by the side of the pitch for around five minutes as police and stewards dealt with the situation.
Ronald Koeman's side travel to Croatia for the return leg next Thursday.