Mujica strongly condemned the way FIFA, football's global governing body, carried out the sanction after Suarez bit the shoulder of Italian defender Giorgio Chiellini.
"We think this will be remembered, this will remain among the worst moments in the history of football. This will be an eternal shame in the story of World Cups," Mujica said in his weekly radio address.
But the Uruguayan leader, who said after the incident that he had not seen a bite, did not condemn the four month ban on all football activities ordered against the 27-year-old Uruguay striker.
"We cannot understand the form, the procedure applied" in making the sanction, the president added.
Suarez bit Chiellini in a World Cup match as Uruguay beat Italy 1-0 to secure a place in the last 16. FIFA ordered a four month ban on all football activities, a nine match international suspension and a 100,000 Swiss francs (USD 112,000, 83,000 euro) fine.
Suarez flew back to Uruguay yesterday.