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 Medel a red card and although Messi did not react he was also sent off, 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 match was continuing, with Argentina going 2-0 up thanks to goals from Sergio Aguero and Paulo Dybala.
Hosts Brazil face Peru in the final on Sunday in Rio de Janeiro.