Judge Francisco Revelo issued a “temporary stay” to Santos, as well as to Colombian armed forces commander Freddy Padilla and former Colombian army chief Mario Montoya.
Ecuador was investigating the three men’s alleged personal and criminal responsibility for the March 2008 cross-border attack on a FARC camp that killed the rebels’ number two, Raul Reyes, and 25 others, including one Ecuadorean citizen.
The incident led to a break-down in diplomatic relations between the two nations, with Ecuador requesting the extradition of the high ranking Colombian military leaders.
Relations between two countries began to improve after talks in September last year.
On Tuesday Colombian President Alvaro Uribe and Ecuadorean President Rafael Correa laid out topics of discussion for their nations to jointly address, following the first meeting of the heads of state since diplomatic relations were broken.