The Barcelona superstar accused the South American governing body of being “corrupt” during the Copa America.
He was already banned one game, a World Cup qualifier, in the wake of the row, but further punishment has been dished out.
Messi will be given a three-month ban from international duty which will see him miss Argentina’s friendlies with Chile and Mexico in September and Germany in October.
The 32-year-old superstar was shown a red card in the third-place play-off against Chile at the start of July. Argentina won the game, but Messi fumed and did not appear on the pitch for the medal ceremony.
When asked why he wasn’t present, he told reporters at the time: “Because we don’t have to be part of this corruption, this lack of respect towards the whole Copa.