Marvin Solano's men were buoyed by a brace from Victor Nunez, which sandwiched a Jose Sanchez goal after Esteban Ramirez's opener.
Jose Ulate scored from the penalty spot late on for a consolation goal for the visitors at the Estadio Eladio Rosabal Cordero.
Limon fell to 11th on the table after Uruguay climbed above them with a 2-1 road win over Puntarenas.
Alajuelense continued to heap the pressure on Herediano, as they earned a 2-0 win at home to UCR to remain within a point of the league leaders - although have played a game extra.
Regardless, both sides - along with Deportivo Saprissa - are bound for the finals series, as they are secure in the top four.
Saprissa were held 1-1 by cellar-dwellers Belen Siglo XXI after Heiner Mora scored late for the struggling outfit.
But fourth-placed Cartagines are no chance of overtaking Saprissa in third, despite chalking up consecutive 2-1 wins over Perez Zeledon - the latest coming at Cartagines' home ground.
Erick Scott haunted Perez Zeledon twice in the space of three days, scoring all four goals against them.
Elsewhere, Santos de Guapiles made it three wins in their past four with a 4-0 rout of Carmelita, who lost their first match in six.
