The parties announced the tribunal on Friday in a joint statement in Havana where negotiators have been holding peace talks since 2012 to yield a final peace agreement, reports Xinhua news agency.
The conflict has killed more than 220,000 people.
A number of important world figures and bodies will be invited to help appoint 24 judges for the court, said the statement released by the Cuban and Norwegian delegations which act as guarantors of the peace process.
Twenty judges will be Colombian while four will come from other nations.
The agreement states that the Revolutionary Armed Forces of Colombia (FARC) and the Colombian Army would abide by any decision made by the court, concerning any crimes committed during the country's civil war.
Anyone admitting any crimes and confessing the truth would receive sentences of restricted freedoms of between five and eight years but would not go to jail, according to the agreement.
Those who do not do so but are found guilty could receive sentences of up 20 years in jail, it added.
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