Oscar Ramirez's men had been put out by their CONCACAF Champions League participation that saw them fall several games behind in domestic action.
But Alajuelense have stormed to the helm of the table, and moved outright first after a 2-1 win over Perez Zeledon followed by UCR's 2-0 loss to Limon.
Luis Sequeira bundled home inadvertently in the 33rd minute, after Perez Zeledon's goalkeeper parried into his path.
Perez Zeledon were level 10 minutes into the second half in Alajuela, after Jorge Gatgens got on the end of a left-wing cross to nod home.
But Jean Carlo Aguero's emphatic finish 15 minutes from time was the difference, the former Costa Rica Under-20 representative scoring his first senior goal for Alajuelense in just his second start for the club.
Aguero took a touch away from goal, before shooting on the turn and finding the bottom left corner.
It was Alajuelense's 10th win in 12 games this season, the leaders still with three games in hand on closest rivals UCR.
Jose Giacone's UCR fell to two second-half goals from Limon's Lemar Hernandez and Jossimar Pemberton.
Deportivo Saprissa's blistering form sees them level on points with UCR, and also with two games in hand, after their fifth straight victory.
A Carlos Saucedo brace helped Saprissa beat cellar-dwellers Uruguay 2-1, moving them to 28 points - two clear of fourth-place Cartagines, who were also victorious.
Cartagines downed Herediano 4-2 to end a two-match losing run, while Carmelita beat Belen Siglo XXI 2-0 to climb above Perez Zeledon into fifth on 19 points.
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