Following an even start to the contest, the home side broke the deadlock in the 21st minute when Thiago Ribeiro fired in from outside the penalty area.
The visitors continued to push for an equaliser after the break and went on control large parts of the possession.
However, their failure to convert their domination into goals was punished 11 minutes from time. Victor Ibarbo threaded a pass through to Mauricio Pinilla, who slotted the ball into the net to seal the victory.
Ibarbo added a third for the hosts in stoppage time from inside the area.