Going into the second leg with a 1-0 advantage, Leon had to wait until the 51st minute against Toluca before sealing their final place.
In doing so they kept alive their hopes of adding to the Apertura title they won in November.
Mauro Boselli and Rafael Marquez both went close for Leon in the opening exchanges, but Carlos Pena made no mistake as he struck the winning goal for Gustavo Matosas' men early in the second half.
They will now face Pachuca in the showpiece after they survived a second-leg comeback from Santos Laguna to progress on away goals, following a 4-4 aggregate draw.
A bad-tempered clash, that saw both sides reduced to 10-men, ended 4-2 on Sunday in Santos' favour, but strikes from Enner Valencia and Dieter Villalpando saw Pachuca edge into the final courtesy of the two goals they had scored in the first leg.
Rafael Figueroa had put Santos ahead before goalkeeper Oswaldo Sanchez was sent off.
That gave Pachuca a way back into the match and they struck twice in quick succession to lead at the break.
The visitors also has a player sent-off when Walter Ayovi received a straight red card just after the hour, and that sparked Santos' comeback.
Juan Rodriguez levelled the match with a 68th-minute penalty before Javier Orozco moved them 3-2 ahead with 13 minutes to play.
They levelled the tie on aggregate when Figueroa netted his second goal of the game in stoppage time but that was still not enough.
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