They arrested at least 12 fans of title holders Corinthians of Brazil after Wednesday night's match against home side San Jose and will be interrogating them to try to identify who set off the flare that hit the boy in the eye, killing him almost instantly.
"I would exchange my world title for the boy's life," said a visibly upset coach Tite of club world champions Corinthians.
Local media said the remains of the flare did not correspond to the kind seen in Bolivia where football hooligans or demonstrators use carton fireworks with no plastic parts, suggesting it may have been brought into the country.
South American football body Conmebol, whose headquarters are in Paraguay's capital Asuncion, told Reuters they were awaiting their match delegate's report before making a statement on the incident.
According to Conmebol's competition rules Corinthians could be kicked out of the present or a future tournament if it is confirmed some of their fans were responsible for the boy's death.
Despite the incident occurring early, the match was completed with San Jose and Corinthians drawing 1-1 at the Jesus Bermudez stadium in Oruro, a mining city 3,700 metres above sea level, in their Group Five debut.
The boy was identified as Kevin Beltran, a San Jose supporter, and angry Bolivians in the crowd shouted"murderers"at the Corinthians fans, Brazil's Globo said.
It was not the first death from a flare at a football match with at least two at previous incidents in Barcelona and Buenos Aires.
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 football 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.
Boca fans launched three flares from the home terraces behind one of the goals at the same time. One landed on the pitch, another flew out of the stadium and the third hit Basile on the visiting fans' terraces.
Fans regularly take flares into matches in South America, past lax security checks.