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.
Everton had opened the scoring moments before the trouble broke out in the Europa League play-off first-leg.
The teams waited on the side of the pitch before the police and stewards restored order, and the match resumed after a break of almost five minutes.
The Toffees added a second goal through Idrissa Gueye shortly after the restart and they held on to win 2-0.
The second leg takes place in Split on Thursday.
Uefa has opened disciplinary proceedings against Everton and Hajduk Split following the crowd trouble that marred Thursday's Europa League match.