"The armed forces, in cooperation with allied forces, liberated the city of Deir Ezzor completely from the clutches of the Daesh terrorist organisation," the military source said.
Islamic State had for years besieged a government enclave in the city until the army relieved it in early September, starting a battle for the jihadist-held parts of the city.
The army captured al-Hamidiya, Sheikh Yassin, al-Ardhi and al-Rashidia districts in recent attacks and the al-Hawiqa district was the last to be held by the jihadists, a military media unit run by the army's ally Hezbollah reported.
Deir Ezzor, on the west bank of the Euphrates, is the largest and most important city in eastern Syria. It is the centre of Syrian oil production.
An offensive by the army, backed by Russia, Iran and Shia militias, and a separate offensive by US-backed Syrian militias have pushed Islamic State back into a shrinking pocket of land downstream of Deir Ezzor near the Iraqi border.