The president of Chile's Football Federation (ANFP), Sergio Jadue, has condemned the side's supporters for their 'shameful' misconduct ahead of the 2-0 win over Spain at the Maracana on Wednesday.
A large group of fans forced their way into the stadium via the press room in an attempt to see their side in action against Vicente del Bosque's men in Rio, but were eventually held back by stewards and 87 detained by state authorities.
Those fans were given 72 hours to leave Brazil in accordance with the local law, but Jadue revealed there will also be a Fifa investigation into the events on Wednesday.
"I was informed about what happened and it's shameful," he told reporters in Belo Horizonte on Thursday.
"I spoke to the Chilean ambassador in Brazil. We've already had an investigation opened by Fifa for the throwing of flares in the game against Australia. That document has been replied to by our lawyers. Now there will be another one."
And he added: "What went on yesterday should never happen again."
On a more positive note, however, the Chile chief was delighted with his side's success against Spain and believes the South Americans are no longer in awe of the world's top teams.
"Chile are no longer afraid of the biggest teams and we are in the process of becoming one of them," he said. "Our common objective now is to go on making history - for our football and for our fans."
After eliminating Spain on Wednesday, Chile will meet Netherlands in their final group game on Monday to decide which of the two teams tops Group B.
"For us it's important to win the group," Jadue said. "Not just for us, but also for our players, who are protagonists in the world's top leagues."