The Syrian Democratic Forces commander-in-chief said last Thursday that his force would declare victory within a week.
The SDF has previously estimated several hundred terrorists-believed mostly to be foreigners-to be still in Baghouz, and the USA -led worldwide coalition has described them as the "most hardened" terrorists.
The SDF has said that those who did not use last week's humanitarian window to be evacuated were essentially chosing to die in Baghouz.
"They still hold civilians and are lacing the tunnels with IEDs (improvised explosive devices) as well".
Fighters of Syrian Democratic Forces (SDF) stand together near the village of Baghouz, Deir Al Zor province, Syria, on March 1, 2019.
The Syrian Democratic Forces (SDF) clashed with Islamic State (IS) for almost 18 hours inside Baghouz after removing the remaining civilians and resuming their assault on Friday evening.
Afrin said the buffer area between IS and SDF had been closed after the SDF's advance.
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"ISIS fighters have been using suicide vests and vehicle bombs to slow down the SDF offensive and hide from Coalition strikes in the area of Baghuz", Col. Sean Ryan told Reuters.
It was the final batch, according to Bali, who said only jihadists remained holed-up inside the shrinking redoubt. "The threat remains as long as Daesh (IS) fighters have not given up in Baghuz and have the will and weapons to fight".
The evacuees on Friday included wounded men but were mostly women and children. There were Russians, Indonesians, Bosnians, Dagestani, Kazaks, Egyptians, Syrians and Iraqis.
"Since the start of the fighting, we have taken 13 or 14 positions from them", the commander told an AFP reporter outside Baghouz early Sunday. They dragged along few belongings, distraught children and broken spirits. "There are many fighters and families inside", she said. "ISIL is weak only in Baghouz but elsewhere it is expanding and growing".
The capture of Baghouz would mark the end of IS territorial control in the region and deal a death blow to the "caliphate", which once covered huge swathes of Syria and Iraq.
The United States has about 2,000 troops in Syria, mainly to support the SDF in fighting ISIS. In the last week alone, 13,000 people, majority women and children, arrived at the al-Hol camp in Hassakeh province which now houses approximately 45,000 people, according to the United Nations. Air strikes destroyed two of them, and the SDF fired on a third to blow it up, he said.
Those fleeing described a desperate situation for civilians, with widespread reports of civilians killed and injured, destruction of civilian infrastructure, and shortages of food, a U.N statement issued in Damascus said.