Toluca lost 2-1 to America on Sunday, but advanced to the final 3-2 on aggregate, while Tijuana defeated Leon 3-0 to go through 3-2 over the two legs.
Toluca will be attempting to equal Chivas with 11 Mexican league titles when it takes on Tijuana in the first leg of the final on Thursday in Tijuana. The return leg will be played next Sunday at Toluca.
America, trailing 2-0 from Thursday's first leg, dominated the first half of the return leg Sunday, getting goals from Miguel Layun in the 16th minute and Daniel Montenegro in the 37th to draw level with Toluca on aggregate.
But two halftime substitutions from Toluca coach Enrique Meza changed the tone of the game, with Edy Brambila and Edgar Benitez both coming on and making an immediate impact.
Benitez scored in the 59th to give Toluca the goal it needed to advance to the final.
Benitez also scored in Thursday's first leg to help Toluca win at Estadio Azteca. Lucas Silva had the other goal in that game.
Fidel Martinez opened the scoring for Tijuana in the 42nd minute when his left foot shot from inside the area found the far corner of the net.
Colombian Duvier Riascos made it 2-0 with a goal in the 68th and Richard Ruiz got the third in the 90th to send Tijuana through to the final.
Leon had won the first leg 2-0 at home, with Othoniel Arce and Carlos Pena scoring within one minute of each other.
Tijuana was formed as a club in 2007 and only promoted to Mexico's first division in May 2011.
Toluca, Tijuana, Leon and America will all represent Mexico in the Copa Libertadores.
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