The Liga MX outfit, two-time winners of the tournament when it was known as the Champions' Cup, completed a convincing 3-0 aggregate victory.
Carlos Esquivel opened the scoring and Juan Manuel Salgueiro added a second after the interval at the Estadio Nemesio Diez.
Champions in 1968 and 2003, Toluca were also runners-up in 1998 and 2006.
They will face either Tijuana or Cruz Azul in the final, with the former holding a 1-0 lead heading into their second leg on Wednesday.
Kevin Sancho's dreadful attempted clearance from right-back on 35 minutes cost Alajuelense the opener.
Esquivel picked up the poor attempted pass, cut inside from the left before his deflected finish found the bottom corner.
Salgueiro doubled their lead on the night and tripled it in the tie after a scrappy goal in the 62nd minute.
When Jonathan McDonald was sent off for the visitors five minutes later, their chances of a miracle comeback were over.
It ended the Costa Rican side's run after they reached the last four in the Champions League for the first time.
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