The flares appeared to come from the Croatian supporters' section. UEFA are certain to open an inquiry into the incident and the country has a record of trouble in recent months.
Croatia were leading 2-1 when English referee Mark Clattenburg halted proceedings so the flares could be extinguished.
One of the flares appeared to explode as it hit a member of the stadium's staff dealing with another pyrotechnic.
Croatia captain Dajijo Srna ran to the Croatia corner of the stadium to appeal for calm. But punches were then thrown between fans before stewards calmed the situation.
FIFA slams 'shameful scenes' at Euro 2016
UEFA deducted one point from Croatia and ordered the country to play two European Championship qualifying matches behind closed doors after a swastika was painted on the pitch before a qualifying match against Italy last year. The Croatian federation was fined 100,000 euros.
UEFA also barred Croatia from playing qualifiers in the city of Split, which hosted the 1-1 draw with Italy on June 12 last year, when the Swastika was clearly seen on the pitch.
The flares were the latest stadium trouble at Euro 2016.
Russia were threatened with disqualification from the tournament after their fans crossed barriers to try to attack England fans in Marseille last Saturday.
The Russians were found guilty of crowd disturbances, racist chants and throwing firecrackers.
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