Merseyside Police detained one man after trouble flared during Thursday night's Europa League playoff tie between Everton and Hajduk Split at Goodison Park.
The disturbance occurred in the away end during the first half of Everton's 2-0 win, with missiles being thrown and advertising boards kicked over as supporters surged towards the pitch.
As stewards and police moved to try to bring the situation under control, the players were instructed to leave the field by referee Ivan Kruzliak and the game was halted for several minutes.
The man was detained for pitch encroachment but no further arrests were made, Merseyside Police confirmed, and the rest of the match and its aftermath passed by without notable incident.
Police had anticipated the potential for trouble, with policing levels similar to those for the Merseyside derby against Liverpool.
UEFA later announced the opening of disciplinary proceedings against both clubs.
A statement said Everton had been charged with the throwing of objects while Hajduk are accused of throwing objects, crowd disturbances, field invasion and acts of damages.
Hajduk Split have already been sanctioned during this season's Europa League qualifiers for the behaviour of their supporters. UEFA ordered a partial stadium closure for the home leg of their third-round qualifying clash with Brondby following racist chanting by supporters in the previous round against Levski Sofia.
Hajduk Split were also fined €30,000 euros for the chanting and a further €5,000 euros for the throwing of objects. Their fines over the last decade total more than €700,000 euros.
Michael Keane's header had given Everton the lead in the 30th minute just prior to the trouble, and Idrissa Gueye doubled the advantage in the 45th minute.
Regarding the crowd trouble, manager Ronald Koeman said: "I was disappointed. I like to have it really fair, that you can play football, and we needed to stop. I don't know what happened, it was in the corner."
Everton will travel to Croatia for the second leg next Thursday, with a place in the group stage at stake.