Chilean striker Humberto Suazo grabbed a last-minute winner on the night for an exuberant Monterrey who had won the first leg 4-3.
A passionate home crowd roared on Cruz Azul in the first half but despite dominating possession were unable to create real chances.
The best effort in the first half came when Cruz Azul midfielder Cesar Villaluz crashed a long-range drive against the Monterrey crossbar.
After their entertaining, goal-filled first leg, it was a more tactical and midfield-dominated tussle early, but the game opened up after the break.
Monterrey took the lead in the 54th minute when Suazo, who has been linked with a move to Europe, created space for himself on the edge of the area and whipped in a cross which Aldo de Nigris headed in at the back post.
It was a reminder that Suazo, the top scorer in South American World Cup qualifying, can create as well as convert and it gave Monterrey a two-goal cushion for the league title.
The advantage was cut back after a corner in the 77th minute, however, when Alejandro Castro rose for a superb angled header to bring Cruz Azul, hoping to end a 12-year title drought, an equaliser.
Pushing to erase the single goal deficit for the title, Cruz Azul threw men forward in the final stages but were caught on the break in the final minute.
Suazo raced on to a ball over the top and slotted past the advancing Jose de Jesus Corona to start the celebrations.
The defeat was a bitter disappointment for Cruz Azul who have not won either of Mexico's annual titles in the past 12 years but lost finals twice in 2008.
