Rajapaksa departed on Saturday night on a state visit to Qatar.
Sarath Fonseka is currently serving a three-year jail term having been convicted by the high court in what was termed as the 'white flag' case.
He was charged of causing public disaffection of the state through his statement that the senior defence establishment had ordered killing of LTTE formers who turned up at the Army with white flags during the final day of the military clashes in May 2009.
Expectations for Fonseka's release mounted when his wife Anoma Fonseka said Rajapaksa had expressed desire to release the army chief.
Fonseka the military chief credited for government forces' win over the LTTE fell out with his commander-in-chief Rajapaksa immediately after the war ended.