Pachuca beat Monterrey 2-1 away in the second leg of their tie to advance 3-1 on aggregate. Monterrey won the Apertura in the first half of the season.
Morelia upset Guadalajara, who won their opening eight matches of the Clausura, 1-0 away for a 5-2 aggregate victory.
"The team played very good football in the two matches against Monterrey so we're very relaxed today advancing to the semi-finals," Pachuca coach Guillermo Rivarola said.
Monterrey took the game to Pachuca from the start at their Tecnologico ground and went ahead through Paraguayan midfielder Osvaldo Martinez after half an hour.
Midfielder Edy Brambilla equalised with a header from a corner right after halftime following an error by goalkeeper Jonathan Orozco.
The home side could have gone 2-1 up with nearly an hour gone but Martinez had a penalty saved by Rodolfo Cota and Pachuca took control after that, scoring again through substitute Luis Montes with three minutes remaining.
At the Jalisco stadium in Guadalajara, the home side never looked like overcoming their 4-2 deficit from the first leg and Morelia midfielder Elias Hernandez scored the only goal in the 57th minute.
Guadalajara, looking as if they had their minds on the South American Libertadores Cup quarter-finals, had defender Hector Reynoso sent off four minutes from time after he hit substitute Miguel Angel Sansores with his knee.
Necaxa, champions three times in the 1990s, won promotion back to the top flight.