Jose Antonio Giacone's men occupied fourth spot heading to the final matchday, but needed all three points to ensure fifth-placed Carmelita would not reel them in to take their post-season spot.
And away from home, UCR delivered the goods against Santos - with Mauricio Montero's 16th-minute opener followed up by a second-half brace to Jameson Scott.
Santos de Guapiles' miserly form saw them finish the campaign with eight straight losses.
UCR finished four points clear of Carmelita in fifth, after the latter slumped to a 3-1 loss at Herediano.
Carmelita had put some early pressure on UCR, as they took the lead over Herediano after 20 minutes when Carlos Clark scored.
But a penalty on the stroke of half-time for Herediano, converted by Jorge Arias, pulled the hosts back into the game.
Yendrick Ruiz put Carmelita ahead on 68 minutes, and 15 minutes later the points were sealed when Oscar Granados netted.
Herediano finished third in the table, behind second side Alajuelense and leaders Deportivo Saprissa.
Alajuelense fought back for a 1-1 draw at home to Perez Zeledon, while Saprissa fell to a 1-0 loss on the road to Cartagines.
Belen Siglo XXI came from behind twice to earn a 2-2 stalemate at home to Uruguay, with Allan Duarte scoring a brace for the hosts.
Puntarenas finished bottom of the league, after a final-day 1-1 draw with Limon.
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