Godin was shown two yellow cards in two minutes during the final stages of Atletico's 1-0 win over Eibar on Saturday for taking his protests towards the officials too far.
The Spanish football federation's competition committee handed the Uruguayan international a two-game ban on Wednesday on top of the automatic one-match suspension for a red card.
Godin will miss Atletico's final two La Liga games of the season against Real Betis and Athletic Bilbao and their first league game of next season.