The two, Cesar Rivera and Jonathan Diaz, were captured by the rebels in the eastern border region of Arauca.
Three others, including a Colombian general, were taken in a separate incident and remain captive.
The Colombian President, Juan Manuel Santos, suspended peace talks until the captives were freed.
Mr Santos announced an agreement had been struck to free the five last week, but it is still unclear when the general will be released.
Ruben Dario Alzate is the first Colombian general to be abducted in 50 years of civil conflict.
The International Committee of the Red Cross (ICRC) played a part in the handover of the two freed soldiers.
“An ICRC medic part of the mission checked on the soldiers to make sure they were fit to travel,” said the ICRC in a statement.
“They were transported in a helicopter with the ICRC logo to Tame, Arauca, where they were handed over to representatives of the Army.”
The Farc had accused the Colombian government of making the releases difficult by conducting military operations in the area.
