In what was a fiery game at the Estadio Allen Riggioni Suarez on Wednesday, hosts Carmelita scored two goals in as many minutes to collect all three points.
Victor Chavarria opened the scoring in the 65th minute before team-mate Ignacio Quesada struck just 60 seconds later.
Both sides finished the game with 10 men after Carmelita's Verny Ramirez and Uruguay's Andres Rodriguez were shown their second yellow cards late in the game.
The result left Uruguay winless after their opening three games while Carmelita move to third on the table on six points, three adrift of league leaders Deportivo Saprissa.
Meanwhile, Limon and Puma Generalena both picked up their first points of the season after playing out a 0-0 draw on Thursday.