Substitute Angel Sepulveda also scored twice in the final quarter of an hour for Morelia, who ended the match with nine players having fought back from three goals down, but could not prevent Santos from going through.
The aggregate score of the semi-final tie was 4-4 after Morelia won the first leg 2-1 at home in midweek but Santos qualified by virtue of having finished higher in the league standings before the knockout phase.
Looking for their first title since the 2008 Clausura, Santos took the lead just past the half-hour when defender Joel Huiqui brought down Oribe Peralta and midfielder Juan Rodriguez converted the penalty sending Morelia's goalkeeper Federico Vilar the wrong way.
Sepulveda put Morelia back into the match in the 74th minute when he headed home from midfielder Edgar Lugo's cross.
