The top-of-the-table clash was not as one-sided from the outset as the score suggested, as the first half ended goalless at the Estadio Eladio Rosabal Cordero.
But Herediano took control of the game in the space of three minutes, as a Kendall Watson own goal in the 54th minute was followed by Verny Scott's strike to give the hosts in Heredia a healthy buffer.
Leandrinho added the third goal in the 90th minute, as Herediano went top on 39 points through 18 matches - with Saprissa slipping to second on 37.
Alajuelense kept themselves in the title race, as they had a 2-1 win away at Belen Siglo XXI to keep them within four points of the league leaders in third spot.
UCR chalked up consecutive victories, as they disposed of Uruguay 2-0 on the road to go fourth on 24 points - level with fifth-placed Cartagines, who were beaten 2-1 by Santos de Guapiles.
Carmelita are one point back in sixth, after their 2-1 road win over Limon, who have lost three of their past four to be 11th on 16 points.
Perez Zeledon earned a point away at Puntarenas in a 0-0 stalemate.
