The result gave La Liga a 3-2 aggregate triumph in the two-leg series, as well as its 28th title -- one behind the record mark held by Saprissa - and a berth in the 2013/14 CONCACAF Champions League.
Alajuelense won the first leg 2-1 on December 16 in Heredia, but the return match proved to be a more difficult proposition.
Herediano took a 1-0 lead in the 88th minute, when Ismael Gomez converted a penalty kick after Luis Valle took down the nimble Enoc Perez in the box.
With the aggregate score even at 2-2, the game went to extra time.
Alvaro Sanchez clinched the title for Alajuelense, though, in the 110th minute, directing a shot inside the left post from six-yards out after a chaotic scramble inside the Herediano area.
La Liga, which ended the season on a nine-game unbeaten run, has appeared in three previous editions of the CONCACAF Champions League with its most recent participation being this year. It also won the CONCACAF Champions Cup in 1986 and 2004.
Despite the domestic setback, Herediano has reached the 2012/13 Champions League quarterfinals, where it will meet the LA Galaxy in a two-leg series on March 7 and 13.
Costa Rica - 2012 Torneo Invierno Final, Second Leg
December 22, 2012 (Alajuela, Costa Rica - Estadio Alejandro Morera Soto Scotiabank)
Alajuelense 1 (Álvaro Sánchez 110')
Herediano 1 (Ismael Gómez 86')
Alajuelense: Patrick Pemberton; José Salvatierra, Johnny Acosta, Elías Palma, Cristopher Meneses, Cristian Oviedo (Juan Gabriel Guzmán 58'), Luis Valle, Jorge Davis (Anderson Andrade 73'), Allen Guevara (Álvaro Sánchez 95'), Diego Calvo, Pablo Antonio Gabas.
Herediano: Leonel Moreira; José Garro, Waylon Francis, Pablo Salazar, Marvin Obando, José Miguel Cubero, Elías Aguilar (Ismael Gómez 56'), Carlos Hernández (Esteban Ramírez 70'), Marvin Angulo (Diego País 82'), Enoc Pérez, Yendrick Ruíz.