Messi and Argentina came flying out of the blocks in Arena Corinthians, after tasting elimination in controversial circumstances at the hands of Brazil on Tuesday.
After just 12 minutes the Albiceleste went ahead, Sergio Aguero converting past Gabriel Arias in the Chile net after latching on to a brilliant quickly taken free-kick from the Barcelona wizard.
Injury to Alexis Sanchez and a goal for Paulo Dybala compounded the Roja's woes, finding themselves 2-0 behind after barely 20 minutes.
But both teams were soon to be reduced to 10 men as tensions in Sao Paulo boiled over.
A seemingly innocuous scuffle between Messi and notoriously bad-tempered Chile hardman 'Pitbull' Medel quickly escalated into a full-on brawl towards the end of the first half.
And while Leo certainly helped provoke his opponent by pushing and harrying him past his own goal-line, the Argentina captain was largely motionless when Medel came back throwing his shoulders and forehead repeatedly into his adversary's person.
Referee Mario Diaz, however, deemed both parties equally responsible for the clash, lifting his red card twice and sparking more protests that involved almost every player on the pitch.
There was momentary doubt over whether Messi's punishment would be downgraded to a yellow upon review by VAR; the decision stood, however, and the captain let slip a wry laugh as he vacated the pitch.
Messi's expulsion will only further heighten Argentine suspicions that they have been given a raw deal by officials at this Copa America.
In the Brazil clash the Albiceleste were left incensed after referee Roddy Zambrano declined to consult with VAR over two strong penalty appeals, one of which led directly to Roberto Firmino's goal to put the hosts 2-0 up.
The Argentine FA subsequently filed an official complaint over the standard of refereeing, while coach Lionel Scaloni complained his team had played against "eight men in black" as well as the Brazil team and partisan home crowd.