The Guatemalan club has full control of its CCL destiny after a second win against a North American team.
Heredia previously defeated the Montreal Impact, and another three points against San Jose put the Juguares firmly in control of Group 5.
Heredia scored in the 68th minute. As players from both sides looked at the referee following a collision on the edge of the area, Enrique Miranda kept playing. The 22-year-old forward collected the ball on the edge of the box and powered a shot past David Bingham inside the far post.
San Jose's next CCL bout will be on Sept. 17, when it hosts Montreal.