With a 2-1 aggregate score, Santos Laguna eliminated Atlas from the Liga MX playoffs at the quarterfinal stage.
American striker Herculez Gomez started the second match of the series and went 90 minutes in the win. Previously, Gomez had come on in the 82nd minute of the first leg to play out the final minutes.
The opening leg, in Torreón, Mexico, ended scoreless, with Santos spurning a series of open chances. Mexican international Oribe Peralta sat out both matches through injury.
In Guadalajara, Atlas took the lead early when Omar Bravo, coming back from the injury which relegated him to a spot on the bench in the opening leg, finished off a chance at the far post following an Oswaldo Sanchez save. Sanchez managed to palm Bravo's shot away, but replays showed that the ball had crossed the line and the goal stood.
The equalizer came a quarter hour into the match. Youngster Andres Renteria poked home after Atlas goalkeeper Miguel Pinto and midfielder Lucas Ayala failed to clear properly after a save.
The referee had to make a second telling decision midway through the first half. Facundo Erpen headed back to Pinto, who had raced outside the box. Pinto handled, and the referee ejected him.
Atlas, a man down, knew a scoring draw favored Santos because of away goals.
Carlos Darwin Quintero capped the end-to-end affair by finishing off a counterattack after an hour.
With two minutes remaining in regulation time, Jahir Barraza put the ball in the back of the net, but the referee whistled Omar Bravo offside in the buildup. Quintero killed any chance of a comeback with another counterattacking goal, this one coming just as the clock edged into stoppage time.
Gomez injured his face and had to wear a rather conspicuous bandage through a large section of the match.
Santos, which last won the Liguilla in the 2012 Clausura, will face Cruz Azul in the semifinal.
Follow ZAC LEE RIGG on or shoot him an email