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Chile said it had proof that Barcelona of Guayaquil full-back Byron Castillo was born in Tumaco, Colombia, in 1995 and not in the Ecuadorean city of General Villamil Playas in 1998 as stated on his official papers.
Brazil were unbeaten in 11 games and topped Group B, while Chile finished only fourth in Group A.
The result ensures that with one round of group games still to play, Paraguay qualify from Group A along with Chile, Argentina and Uruguay.
Paraguay went behind to an early penalty but scored three times in the second half for a 3-1 win over Bolivia.
The draw means Argentina are unbeaten at home against Chile in 35 matches, and have gone 12 games without defeat since losing to Brazil in the 2019 Copa America semifinals.
The 31-year-old, who has played 100 games for Chile and scored 24 goals, will sign a three-year deal after having a medical in the next few days.
The country's union of professional footballers threatened to make an official protest to the South American Football Confederation over the "glaring lack of criteria" used in the decisions.
The Chilean’s lawyers have filed a complaint to Spain’s player’s union (AFE) citing an unpaid bonus of 2.4 million euros (2.05 million pounds).
Peru, who last won the Copa America in 1975, will play Brazil at the Maracana stadium in Rio de Janeiro on Sunday.
Reigning champions Chile will face either Uruguay or Peru in Wednesday's semifinal in Porto Alegre.
Results 11-20 of 25