The referee Marco Antonio Ortiz signaled the penalty in favor of Guadalajara del Atlas after the Argentine goalkeeper Nahuel Guzmán fouled the Ecuadorian Aníbal Chalá inside the area.
Atlas increased their lead in the 60th minute with a powerful left-footed shot from Reyes from outside the area after receiving a pass from Furch.
Tigres came close to discounting in the 76th minute with a shot by Argentine Guido Pizarro that hit the post after a deflection by Colombian goalkeeper Camilo Vargas.
Quiñones scored the third goal in the 90th minute with a placed shot from outside the box on a counterattack play.
The series will be defined on Saturday when Tigres is local at the University Stadium in San Nicolás de los Garza, Nuevo León.
In the other semifinal, America will face Pachuca on Thursday, and the key will be defined on Sunday at the Hidalgo stadium, home of the “Tuzos” of Pachuca.