It took until the 76th minute for Alajuelense to take the lead through Alejandro Aguilar's strike but Carmelita hit back on 88 minutes with Carlos Clark's spot-kick levelling the match.
But Alajuelense showed the kind of resilience that earned last season's title as Armando Alonso secured the winning goal in the 90th minute.
Beaten finalists Herediano also had a scare before eventually claiming a 3-1 win at Uruguay.
Johan Condega put Uruguay into the lead after the first minute as Herediano were caught napping from the kick-off.
Herediano worked hard to get back into the match and secured an equaliser in the 37th minute through Olman Vargas.
The momentum continued in the second half with Jorge Arias and Francisco Calvo each scoring for Herediano to secure the victory.
In other matches, Belen Siglo eased to a 2-0 triumph over Puntarenas while Limon and Santos de Guapiles fought out a goalless draw.
UCR and Cartagines shared the points in a 1-1 draw and Perez Zeledon snatched a 2-1 win at Deportivo Saprissa.
