Martha de Lizcano, his wife, said that the operation had brought to end "eight years of great suffering".
Lizcano has been transported to Cali for a medical examination since his health is delicate, Cesar Velasquez, a spokesman for the president's office, said.
The operation follows the rescue of Ingrid Betancourt, a former presidential candidate, three Americans and several other hostages, in July.
Farc has been fighting government forces in the Latin American country since the 1960s, but isa believed to have been seriously weakened by a security operation launced by Alvaro Uribe, the Colombian president.
Three Farc commanders have been killed during the past year and hundreds of fighters are reported to have deserted. Howver, scores of hostages are still being held by the group
Uribe has received billions of dollars in US military and counter-narcotics assistance to tackle Farc and the cocaine trade that has helped fuel the conflict.