The match was 34 minutes old when Chilean captain Gary Medel shepherded out a ball near his own goal. Messi challenged him from behind and Medel reacted angrily, pushing the Argentine and raising his hands.
The Paraguayan referee showed both Medel and Messi red cards, prompting boos in Sao Paulo’s Corinthians arena.
It was only the second red card of Messi’s career, the first also coming while playing for Argentina on his debut against Hungary in 2005.
The referee also showed seven yellow cards in a match that was broken up with 37 fouls.
Sergio Aguero put Argentina 1-0 ahead after 12 minutes and Paulo Dybala made it two 10 minutes later with a nice finish after Giovani Lo Celso had put him through on goal.
Arturo Vidal pulled one back for Chile from the penalty spot 14 minutes into the second half.
Hosts Brazil face Peru in the final on Sunday (July 7) in Rio de Janeiro.
(Production: Mussab Al-Khairalla)