Everton won the match 2-0 but trouble flared after 33 minutes when fans ran on the pitch to throw missiles and kick over advertising boards.
Referee Ivan Kruzliak halted the game to allow stewards and police to try and get the situation under control.
Hajduk Split players did their best to appeal for calm with their fans and the match was continued after a five minute stoppage.
Merseyside Police and Everton will hold a normal post-match debrief to decide if any further action is to be taken.
Everton manager Ronald Koeman commented on the crowd trouble and 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."