Goals from Johnny Acosta and Armando Alonso were all Oscar Ramirez's side needed to seal a top-four spot in the Torneo de Invierno.
It also moved Alajuelense six points clear at the top of the 12-team league.
Acosta struck in the 27th minute and Alonso just moments before half-time to give Alajuelense their victory.
Carmelita are eighth, but the loss was a huge blow to their play-off chances.
Herediano took a step towards the play-offs with a come-from-behind 4-1 victory at Puma Generalena.
Esteban Granados starred with a brace.
Fourth-placed UCR suffered what could prove to be a costly loss, going down 2-1 at bottom side Uruguay.
Perez Zeledon are lurking just three points behind UCR after a 2-1 win at Limon.
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