"Los Rayados" joined Seattle Sounders FC in the knockout stage after Darío Carreño and second-half substitute Neri Cardozo scored for the home side, and Municipal defender Pablo Solorzano tallied an own-goal to send Monterrey to the final eight with a match left to play.
It took Monterrey just 13 minutes to assume control of the match in front of boisterous home crowd of 24,721 at Estadio Tecnologico.
Carreño collected a ball from midfield and embarked upon a solo run down the right side of the penalty area. He cut inside onto his left foot and slid a low effort inside Jaime Penedo's near post to open the scoring.
Penedo was instrumental in keeping Municipal close until the second half. The Panamanian goalkeeper repelled dangerous efforts by Jesus Corona, Walter Ayoví and César de la Peña to frustrate Monterrey and preserve some hope for the Guatemalan side.
The second half started in similar fashion as Penedo produced two more stellar stops to keep Municipal within a goal, but an unfortunate deflection beat him in the 53rd minute. Darvin Chavez salvaged a poor clearance and squared a through ball toward the six-yard box. Solorzano scuffed his attempted clearance and watched as the ball deflected past Penedo.
A rare injury to a member of the officiating crew interrupted the match for several minutes inside the final half hour. Referee Jose Pineda suffered an apparent hamstring injury during the run of play and received treatment on the sidelines for several minutes. He ultimately limped off before being replaced by fourth official Erick Andino to complete the match.
Monterrey made two substitutions as play resumed and both played a part in the final goal in the 81st minute. The sweeping move started when Sergio Perez made an overlapping run past substitute Ángel Reyna into space on the right flank.
Reyna hit his pass into the perfect spot for Perez to drive a low cross toward the near post. Cardozo settled after an attempted clearance deflected to his feet six yards from goal and stroked home to seal the victory.
Monterrey will complete Group 7 with a visit to Panama to face Chorrillo on October 23, but Municipal finished its participation with six points from four games.