UEFA has fined Croatia 100,000 euros (£77,000) after the crowd trouble during their Euro 2016 match against the Czech Republic on Friday.
Referee Mark Clattenburg took the players off the pitch in Saint-Etienne after fans in the Croatia end started throwing flares in the 86th minute.
It is the second biggest fine handed out at the tournament after Russia were fined 150,000 euros last week.
The Czech Republic scored a late penalty to draw the Group D game 2-2.
During the delay, some Croatia players went over to the fans to ask them to stop and a steward appeared to be hurt when a firework he was removing from the pitch went off.
It was thought that the fans were protesting against Croatian Football Federation vice-president Zdravko Mamic.
Mamic was arrested last July, and subsequently charged with embezzling money from Dinamo Zagreb when he was the club's chief executive, an accusation he denies.
The controversy surrounding Mamic has led some Croatian fans believe the federation is corrupt.
Meanwhile, Torcida Split 1950, a Hajduk Split supporters' group, has posted on Facebook that it intends to disrupt Tuesday's Group D match against Spain in Bordeaux.Watch The Premier League Live!! with EXPRESSVPN the #1 Trusted Name in VPN