Their holding midfielder Marco Estrada was sent off in their 2-1 defeat by Spain in Pretoria on Friday night, and central defenders Waldo Ponce and Gary Medel both received their second yellow cards of the tournament.
Estrada's suspension for the match against Brazil in Johannesburg on Monday evening is no big deal - he would almost certainly have been dropped anyway in favour of Carlos Carmona, who returns from suspension.
But the loss of Ponce and Medel is huge. Both have been rock solid at the heart of the Chilean defence.
According to FIFA, which uses tracking technology to capture data on each player at the World Cup and then assesses it to see if it had a positive or negative impact on their team, Ponce and Medel were the two most effective players in the tournament during the first two matches.
Pablo Contreras and Ismael Fuentes are likely to replace the two centrebacks but although both have plenty of experience, they lack the calibre of Ponce and Medel.
The prospect of facing any team without your two first-choice centrebacks is bad, but when that team is Brazil it is terrifying.
Despite their predicament, however, the Chileans have not lost faith in their ability to reach the last eight of the World Cup for the first time in nearly half a century.
"Brazil are one of the best teams in the world but I think that if all of us play to our potential we can go through," said Rodrigo Millar, scorer of Chile's goal against Spain.
Team mate Jean Beausejour recalled the last time that Chile faced Brazil, in a World Cup qualifier last September. On that occasion Chile clawed themselves back from 2-0 down to level the match before conceding two late goals to lose 4-2.
"Unfortunately we couldn't win it but we need to take the good things from that match and leave the bad things behind," Beausejour said.
The omens are not good for the Chileans though. Of their 65 encounters with Brazil down the years they have won just seven, and on the two occasions they have met at a World Cup, the Brazilians have won 4-2 and 4-1.
The last of those two meetings was at this stage of the competition at France 98, when two goals apiece from Ronaldo and Cesar Sampaio sunk Chile.
Unsurprisingly, Chilean defender Arturo Vidal chose not to dwell on that memory and said Chile had improved since then.
"It was a different generation and the players we have today have other ambitions," he said. "We finished second in the South American qualifying group for the World Cup this time round, and in 1998 that wasn't the case."
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