Paraguayan midfielder Salvador Cabanas scored two second-half goals to lead America, which had opened with a 3-1 win over Santos. Luis Sandoval had the third goal for the Eagles.
Another Paraguayan, Fredy Jose Bareiro, also had the winning goal for Estudiantes Tecos, beating former New York Red Bull Diego Jimenez and scoring in the 15th minute.
Chilean veteran Rodrigo Ruiz made it 2-0 in the 59th minute.
Estudiantes Tecos and Santos are both 1-1 heading into Saturday's Group A finales at the Home Depot Center.