The Argentina and Barcelona forward 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.
The 29-year-old 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 five matches still to play.
Lionel Messi has been banned for four international matches - just five and a half hours before Argentina's World Cup qualifier against Bolivia kicks off.