The home side started the game well and had the best chance of the opening 10 minutes when Sebastian Fernandez headed just wide of the post from 12 yards out.
Morales was a constant thorn in the side of the visitors in the first half and that continued when he found Erik Hurtado just outside the area, but the striker poked his volley well wide of the post.
The visitors continued to up the ante in the second half and should have taken the lead when Marco Delgado powered an effort at goal, which was flicked on by Erick Torres but his effort went over the bar.
Chivas took the lead in the 81st minute as this time Torres made no mistake with his header from Delgado's cross, nodding the ball past David Ousted at the back post.
The visitors sealed the win in stoppage time when Leandro Barrera rolled the ball into the empty net from 40 yards after Ousted had taken the decision to go up for a corner in the dying seconds.