The men released on Saturday were among more than 100 people arrested over the alleged plot against Chavez.
Authorities said the young men wearing military uniforms were arrested on a ranch near Caracas in May 2004 and were suspected of belonging to a Colombian paramilitary group.
Chavez said they planned to attack the presidential palace. The men had been convicted of military rebellion.
Pedro Carreno, Colombia's justice minister, said at a ceremony for the freed Colombians in the southwestern town of San Antonio that with Chavez's pardon "a beautiful message is being sent to the world".
Chavez travelled to Bogota, the Colombian capital, on Friday to discuss with Alvaro Uribe, his Colombian counterpart, plans to mediate in the country's long-running civil conflict.
"Nothing is impossible when you put your heart into what you do," Chavez said.
"If I had to go to the gates of hell to try achieve the humanitarian accord in Colombia, I'd be willing."
Talks between the hostage-takers and the government have stalled over Farc's demands for a demilitarised zone in southern Colombia where an exchange can take place as well as the release of two of its members held in the US.
Although Uribe initially accepted a proposal by France, Switzerland and Spain for a safe haven, Uribe refuses to pull back troops under Farc conditions, saying it would allow them to regroup and rearm.