Midfielder Diego Estrada secured a 30th minute lead for Saprissa, which they held until the half-time break.
Three minutes after the restart, Santos levelled the game as Cristan Lagos scored this third goal of the campaign.
But the division strugglers could not hold on to a point as Estrada scored his second goal on 87 points to secure the points for Saprissa.
Saprissa now move one point clear on top of the standings from Ajajuelense and also have a game in hand, while Santos have only one win from eight games and languish in ninth position.
Jerry Palacios' hat-trick allowed his Alajuelense side to keep pace with Saprissa as they swept aside Cartagines 4-0 in front of their home fans.
The Honduran international struck in the fifth and 22nd minutes before completing his treble two minutes after half-time.
Alvaro Sanchez completed the rout in the 82nd minute.
In other results, Heradiano were powered by Yendrick Ruiz's brace as they overcame Perez Zeledon 3-1 and Limon won 2-0 at rock-bottom Belen Siglo XXI.
Uruguay drew 2-2 with Carmelita and Puntarenas fought out a 1-1 deadlock with UCR.
