UEFA said Croatia's federation had been charged over the setting off of fireworks, the throwing of objects, crowd disturbance and racist behaviour.
Turkey face charges of setting off fireworks, throwing objects and invading the pitch.
The Croatian federation has a chequered recent disciplinary record.
Flares were hurled onto the pitch during a Euro 2016 qualifier against Italy in November 2014 and the team were ordered to play the return match against the Italians in June 2015 behind closed doors as punishment for racist behaviour during a match against Norway two months earlier.
But even the stadium ban did not prevent disturbance, with a swastika being drawn on the pitch in Split before the Italy match.
UEFA reacted by docking Croatia one qualifying point, ordering them to play two further matches behind closed doors and issuing a 100,000 euro fine.
Croatia coach Cacic said after the match on Friday: ''These people are really scary, that is why I call them hooligans. These are not really Croatian supporters. These are sports terrorists. The main thing our country doesn't want to mess with are these kind of hooligans.
''This is maybe just a question about six to 10 individuals. I hope they can be identified and punished. I hope the Croatia FA is doing everything to prevent this but it is impossible to avoid.
''Ninety-five per cent of our supporters are ashamed in front of Europe, the players are very sad that after playing a beautiful match this happens.''
Barcelona midfielder Ivan Rakitic fears the team could be thrown out of Euro 2016 after the crowd trouble.
''We have to see if we will play against Spain, maybe they will send us home after this,'' he told HTV.
''There are a lot more fans that love the national team and they will not be able to see Croatia play.
''It is hard to say, but we feel more comfortable playing away... we were lucky that the match went on, the referee wanted to end it immediately.''
Russia have already been handed a suspended disqualification from the tournament, which will be activated if their supporters are involved in any more trouble, following disturbances at the end of their match against England at the Stade Velodrome on June 11.
The Czechs equalised with a penalty in time added on against Croatia after the disturbances and former national team coach Slaven Bilic, working for ITV as a pundit, said: ''It's unbelievable what those people are doing.
''The majority of the fans are telling them to not do it. Some of them are there on a mission. It's probably not the last time they'll do it."
The West Ham manager added: ''Back home it's not the greatest league but it's competitive. When there's a big derby between (Dinamo) Zagreb and (Hajduk) Split people are not taking their kids because they know it'll be dangerous.''