Croatia were winning 2-1 at Stade Geoffroy-Guichard when a volley of flares rained down on the pitch, prompting fighting among the Croatian supporters and causing referee Mark Clattenburg to briefly halt the game.
A banner was held up by a small group in the end where the incident took place, with a group of dissidents opposed to the Croatian Football Federation [HNS] believed to be responsible.
After the restart, Croatia's players, who pleaded with the troublemakers to stop, were clearly distracted and conceded an equaliser from the penalty spot in the final few minutes.
Barcelona midfielder Rakitic said he believed the vast majority of the team's followers would condemn those responsible.
"We just have to say sorry to UEFA and the Czech Republic, and all the people around the world who are following this tournament," he said.
"We will try to play the next match in a better atmosphere. I hope UEFA can understand this. In the next qualifiers we'll have to play a couple of matches in empty stadiums [due to previous incidents], and it's because of these stupid supporters."
Rakitic reluctantly acknowledged the disturbance contributed to his team surrendering what had appeared to be a relatively comfortable lead.
"All I can say is that it would be stupid to find an excuse after the match was stopped," he said. "But the situation is clear - It's happened before. After the match restarted they scored and this has some connection. I don't want to talk too much about it, but that's what happened on the field.
"To talk too much about it, it's not easy, after such a beautiful performance from our side. I think we've got more supporters on our side.
"Most fans are supporting this team. They are real supporters. But there are 10 individuals can make all these problems. The Croatian FA, especially [president, Davor] Suker and his colleagues, are fighting against it."