Croatia faces UEFA sanctions following crowd trouble at Euro 2016
The game was held up for around five minutes by English referee Mark Clattenburg whilst the flares were removed from the pitch, with the incident taking place late in the second half.
Croatia had been dominating the game and leading 2-1 at the time of the incident, but the Czech Republic earned and converted a penalty quickly after play restarted.
One steward appeared to be injured by a flare that exploded in his hand, and which also came dangerously close to Croatian goalscorer Ivan Perisic.
Other objects landed near riot police deployed in front of the Croatian section of the ground.
Croatian head coach Ante Cacic later said: "These are not Croatian fans, they are sports terrorists," although there was more behind the story than initially appeared.
VIDEO - Croatia Manager Ante Cacic Hits Out At The "Sports Terrorists" "Hooligans, Not Fans" https://t.co/U6aCwARmS2— Beany (@Beanyman62) June 17, 2016
'Ultras' from Croatia's two biggest clubs, Dinamo Zagreb and Hajduk Split, are believed to be behind the incident. It's known that they have been in conflict with the Croatian Football Federation (CFF) leadership for a number of years.
Throwing flares onto the pitch could have been an attempt to get their national team disqualified from Euro 2016 and put enough pressure on the people they want to step down.
Zdravko Mamic, the former Dinamo Zagreb chief executive, is reported to be their main target, due to the perceived influence he has on both the national and domestic game.
Croatian ultras have a long history of trouble-making at the national team's matches. Croatia have been fined on several occasions in recent years due to disturbances including riots, clashes with police, racism and pitch invasions.
The most infamous case was the swastika mowed onto the pitch in Split the night before the Euro 2016 qualifier versus Italy one year ago.
Flares were also thrown onto the pitch in Milan in the reverse qualifier, and the incident resulted in two matches played behind closed doors for Croatia.
The CFF Executive Committee released an official statement the day after the latest trouble: "The Croatian Football Federation, Croatian national football team, Croatian internationals, Croatian football, Croatian fans, and Croatian state have all been disgraced once again at the European stage by a group of hooligans that hold nothing Croatian sacred, and that have ruined a beautiful football festival in Saint-Etienne."