Goals in the final 23 minutes from Bryan Vega and Leandro Adams saw Belen Siglo XXI earn a share of the spoils at the Estadio Alejandro Morera Soto.
Belen Siglo XXI have collected five points from seven matches so far to sit third bottom.
As for Alajuelense - fourth in the standings with 10 points after four games - their perfect start to the season came to an end, having won their opening three fixtures.
Alajuelense broke the deadlock after just two minutes through Ariel Rodriguez.
Pablo Gabas doubled the home side's lead in the 57th minute before Belen Siglo XXI staged a spirited comeback.
Vega pulled a goal back for the visitors in the 67th minute and Adams equalised with seven minutes remaining.
Belen Siglo XXI ended the match with 10 men following a red card to Mauricio Nunez in the closing stages.