Four River Plate players were taken to hospital on Thursday following the incident and Argentina's security chief slammed Boca for failing to protect their rivals during the last-16 second leg superclasico.
He also criticised CONMEBOL for taking more than an hour to abandon the match.
In a statement on Friday, Paraguay-based CONMEBOL said it had "handed the (Argentine) club until 1400 (local time) tomorrow to present its case."
Football in Latin America has a history of fan violence and the situation in Argentina has worsened in recent years with the rise of barra bravas, organised hooligan firms.
Boca president Daniel Angelici said the club was analysing video footage to determine who was to blame for the assault which shocked many supporters already hardened to violence among rival gangs.
"We are using video footage ... to identify quickly and mete out a punishment that sets an example to others, and also to understand why a person would throw a liquid that can hurt players and cause a match to be suspended," Angelici told a news conference.
CONMEBOL must now decide whether to throw Boca out of the tournament.
"We will be respectful of its decision," Angelici said.
PASSIONATE RIVALRY
River players emerged from an inflatable tunnel after the break clutching their faces and rubbing their streaming eyes, with the scoreline 0-0.
The club's medical team said the four players were suffering from inflammation of the cornea and would need days to recover.
"We went to a football match but left as if we had been to a protest," said team doctor Pedro Hansing.
The rivalry between the two Buenos Aires sides is one of the most heated in the world. It pits Boca, a traditionally working-class team, against up-town rivals known as the 'Millionaires'.
Boca's Bombonera stadium was a cauldron of drums and the chants of the club's passionate supporters who sat inches from the touchline separated by wire fences.
Few players relish the visit with away supporters barred from attending matches in a bid to curb violence.
The Bombonera was closed to the public on Friday to allow investigators to examine evidence.
River players were escorted from the pitch under riot shields as missiles rained from the stands. Boca players saluted their fans, drawing condemnation on social media.
River coach Marcelo Gallardo, whose side led 1-0 after the first leg, called the incident "deplorable" and "shameful".
Angelici last night apologised for the fracas but said the players should not be punished.
(Additional reporting by Maximiliano Rizzi in Buenos Aires, Daniela Desantis in Asuncion and Andrew Downie in Berlin, editing by Pritha Sarkar)
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