Copa America officials were forced into removing the trophy after the three-time Balon d’Or winner declined to take Most Valuable Player award, media reports said.
The Barcelona superstar reportedly instructed officials not to award him the trophy at Chile's National Stadium in Santiago on Sunday.
A video has emerged of an official removing the trophy from a stage before the presentation ceremony.
Messi, with a glittering club career, was influential in taking Argentina to the final.
But his only goal in the tournament came from a penalty during Argentina’s 2-2 draw against Paraguay in the team’s opening game.
After that match, the Argentine refused to pick up the man of the match award. Tournament organisers then decided to withdraw the trophy rather than give it to someone else.
The final defeat was Argentina’s first defeat in a major tournament after the Albiceleste lost to Germany in the World Cup final last year.
Messi has been often criticised for failing to repeat his club form for his country.