Ronald Gonzalez's men needed a 94th-minute winner from Ariel Rodriguez to overcome Limon 3-2.
Having played a game more than their nearest rivals, Saprissa are three points clear of UCR, Cartagines and Alajuelense.
Saprissa, who face Real Esteli in the CONCACAF Champions League on Tuesday, fell behind in the 17th minute.
Steven Calderon was on hand to head in a corner from close range to give Limon a surprise lead.
Neeuro Shaquille equalised in the 31st minute with a bit of luck as his attempted cross took a huge deflection and found the back of the net.
Another corner led to another goal for Limon just before half-time as Saprissa failed to clear and Cesar Monge scrambled in.
Saprissa were level just a minute later – and before the break – thanks to a fine 25-yard finish from Juan Bustos.
They had to wait until the dying stages to find a winner, with Rodriguez getting on the end of a cross from the left to earn them three points.
Elsewhere, Allan Duarte's double helped UCR to a 3-1 win over a Puma Generalena side who finished with 10 men.
Cartagines clinched a 1-0 win at Belen Siglo XXI to also move into six points, while Alajuelense are alongside them after a 2-0 victory at Uruguay.
Santos de Guapiles were 2-1 victors at home to Carmelita and Perez Zeledon claimed a 2-1 win over Herediano.
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