Jonathan Sibaja put the visitors ahead in Alajuela, but a fine equaliser came from the head of Allen Guevara as the sides went to the interval at 1-1.
Alvaro Sanchez then fired Alajuelense ahead for good in the 58th minute, as they made it three wins from as many appearances.
Alajuelense trail UCR by four points, although they have three games in hand on the league leaders, who suffered their first defeat of the campaign.
Uruguay's woeful campaign continued, the strugglers losing 2-0 on the road at Santos de Guapiles, who were glad to end a two-game losing run.
Defender Rudy Dawson got the final touch into his own net to hand Santos a fortunate lead in the 11th minute, before the hosts doubled their advantage late on via Cristian Lagos.
Uruguay have just two points from seven league fixtures, and are only off bottom spot due to Herediano's inactivity - the latter having played just twice so far.
Herediano's scheduled visit to Deportivo Saprissa on Tuesday was postponed.
Goals either side of the half-time break to Winston Parks and Jake Beckford helped Limon beat Belen Siglo XXI 2-1, the visitors scoring a consolation penalty late on through Randall Leal.
Puma Generalena bounced back from a last-start loss to Belen Siglo XXI, edging Perez Zeledon 1-0 at home.
Luis Gonzalez's 35th-minute penalty was enough for promoted Puma to chalk up their second win in seven in the top flight, taking them above their defeated opponents into eighth spot.
