The Chivas, rebuilding under former Mexico coach Ricardo La Volpe, needed a win to be among the top eight teams in the 17th and final round of the championship’s league phase.
Neither Guadalajara nor Monterrey made it into the last-eight after defender Efrain Juarez headed the only goal in the 85th minute from a corner taken by Chile’s Humberto Suazo at the Omnilife stadium.
Monterrey finished with 23 points but behind eighth-placed defending champions Leon on goal difference, while Guadalajara were left stranded with 21 points.
Leon, who won the Apertura championship in the first half of the season, will meet Clausura leaders Cruz Azul in the two-leg quarter-finals.
“It’s a bad result, everything looked set for a win today, I think the team had good control but we lacked more chances and to finish them off,” said La Volpe, whose side won one and lost two of their four matches since he took the reins on April 2.
“I took charge with four matches left (in the round-robin phase) and there you have the results, logically we can’t think of failure because that word doesn’t exist in my vocabulary,” the outspoken Argentine known as “Bigoton” (big moustache), told reporters.
“The team needs some reinforcing … but I don’t see big changes. We have young players pushing (for places in the team), but from the middle towards the front we need players with more experience.”
Guadalajara’s arch-rivals America, with whom they share a record of 11 league titles, secured their place in the last eight with a 1-1 draw at Toluca.
“I’m not satisfied, we need to improve and take better decisions but I have confidence in these players. The important thing was to be inside (the knockout phase) and we are, all eight teams have chances of being champions,” said America’s Argentine coach Antonio Mohamed.
Pachuca qualified in dramatic fashion on Friday when they scored four goals in the last quarter of an hour to win 4-3 at Queretaro after trailing 3-0.
Substitute Enrique Esqueda and striker Abraham Carreno scored two goals apiece for the “Tuzos” (moles) with the latter’s winner coming in added time after Queretaro’s Brazilian Ricardo da Silva had put the match seemingly beyond Pachuca’s reach completing a hat-trick in the 66th minute.
The rest of the quarter-final line-up has Toluca against Tijuana, UNAM Pumas versus Pachuca and Santos Laguna meeting America.
(Additional reporting by Carlos Calvo; Writing by Rex Gowar in Buenos Aires; editing by Amlan Chakraborty)