Croatia have been fined €100,000 and told they will be banned from selling tickets to fans identified as hooligans if there is any further trouble during Euro 2016.
Croatian players had to call for calm when a volley of flares rained down on the pitch and halted play in the second half as part of a co-ordinated protest against the Croatian Football Federation (HNS).
The demonstration caused some other Croatia fans to confront those who were protesting, with the HNS later thanking supporters who had tried to stop the trouble as well as calling for authorities to do more to help them.
Following a meeting in Paris on Monday, the UEFA Control, Ethics and Disciplinary Body imposed sanctions on Croatia for the charges of crowd disturbances, use of fireworks, throwing of missiles and racist behaviour.
As well as the fine, Croatia have received a ban from selling tickets to "certain fans identified by the HNS and Croatian authorities as hooligans" that is deferred under a probationary period until the end of the Euros.
Croatia have the opportunity to appeal the verdict.