A Bolivian prosecutor charged two Corinthians fans with homicide and 10 others of trying to cover up for them after the 14-year-old was killed during San Jose's 1-1 home draw against the Brazilian side in Oruro on Wednesday.
"Corinthians have been sanctioned so that all their home matches are [played] behind closed doors in the Libertadores," Nestor Benitez, spokesman for Conmebol, the South American Football Confederation, told Reuters.
"In addition, clubs playing at home against Corinthians have been prohibited from selling tickets for Corinthians' fans. That is to say, their fans wont be able to see the matches at all," Benitez said.
The decision covers the whole tournament, scheduled to end in July, until CONMEBOL's disciplinary committee issues a definitive ruling on the case, Benitez added.
Corinthians said it would appeal the ban using all legal means, calling the punishment "unjust" because it "directly harms the rights of the innocent."
"The measure harms not just the club but principally the more than 80,000 fans who have already bought tickets for the team's three home games in Group 5," Corinthians said in a statement. "They don't deserve that punishment."
Oruro prosecutor Abigail Saba told reporters she had made charges after interrogating 12 Corinthians fans arrested at the match for launching the flare that killed the boy and was meant to celebrate their team's early goal.
Saba said she was investigating "a crime with the death of a minor", Bolivian newspaper La Razon reported on its website.
CONMEBOL's decision is a major blow to Corinthians, the Sao Paulo club that won the Libertadores Cup for the first time last July before beating Chelsea to win the Club World Cup in December.
The ban means their famously passionate fans will be excluded from next Wednesday's visit to Sao Paulo by Colombia's Millonarios and later home matches in Group Five against Tijuana of Mexico and San Jose.
The Brazilians were playing their first match in the defence of the trophy when the incident occurred early in the match after Peru striker Paolo Guerrero gave them the lead in the fifth minute.
The game continued and the teams played out a 1-1 draw with Carlos Saucedo putting San Jose level at the Jesus Bermudez stadium in Oruro, a mining city 3,700 metres above sea level.
The boy was identified as San Jose supporter Kevin Beltran, and angry Bolivians in the crowd chanted "murderers" at Corinthians fans, while the Brazilian team's coach Tite said: "I would exchange my world title for the boy's life."
The club declared a week of mourning and said players would wear black armbands for their next two matches.
Local media said the remnants of the flare did not correspond to the kind seen in Bolivia, where ardent football supporters or demonstrators use carton fireworks with no plastic parts, suggesting it may have been brought into the country.
It was not the first death from a flare at a football match with at least three previous incidents.
In 1993 at World Cup Qualifying game between Wales and Romania in Cardiff, a fan was killed by a flare which was fired across the pitch and into the neck of an elderly man.
Guillem Lazaro, a 13-year-old Spanish boy, was killed in March 1992 by a flare that hit him in the chest at Espanyol's old Sarria stadium in Barcelona on his first visit to a match.
In August 1983, Argentine Racing Club fan Roberto Basile, who was 26, was hit in the throat and killed by a flare shot horizontally the length of the pitch at Boca Juniors' La Bombonera.
Fans regularly take flares into matches in South America, sn
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