Chicago Fire signee Cuauhtemoc Blanco set up Paraguayan Salvador Cabanas for the game's only goal in the 62nd minute.
Regular-season leader Pachuca looked set to return to the Clausura final with a 3-1 win at Cruz Azul on Wednesday night. Cristian Gimenez scored twice for the Tuzos.
Semifinals, First Leg
Cruz Azul 1 (Borgetti pen. 45) Pachuca 3 (Caballero 21, Gimenez pen. 35, 62).
Club America 1 (Cabanas 62) Guadalajara 0.
Semifinals, Second Leg
Guadalajara vs. Club America (Univision, live, 7 pm ET)
Pachuca vs. Cruz Azul (Azteca America, live, 9 pm ET)