The Argentine was punished for directing “insulting words” at an assistant referee in Thursday’s 1-0 win over Chile.
Messi, who scored the only goal in the qualifier, was angered when he was flagged for a foul, waving and shouting at the assistant in response.
He was also fined £8,100.
He will miss his country’s next four competitive fixtures.
Argentina are third in South American qualifying, with the top four teams advancing to next summer’s finals in Russia. There are left with five matches to play.