Erick Scott and Paulo Jimenez scored the goals for Cartagines, as they extended their unbeaten streak in the league to five games and moved above Puntarenas into third position.
The win takes Cartagines to nine points from five games, four points behind Saprissa, while second-placed Herediano are on 10.
Cartagines opened the scoring just before the hour mark on Wednesday when Scott collected a deflected shot and lifted the ball over Limon's goalkeeper Roman Arrieta.
The home side had to wait until the 92nd minute to double their lead with Jimenez lashing a half-volley in off the underside of the bar from the edge of the penalty area.
Herediano stayed ahead of Cartagines with a 1-0 win over Belen Siglo XXI, while Alajuelense moved into fifth on goal difference with a 2-1 triumph over Uruguay.
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