A Syrian Democratic Forces commander said the jihadists were caught overnight as they attempted to slip out of Baghuz with the help of smugglers.
Hundreds of others have surrendered and been evacuated from the village with thousands of civilians in recent days.
It comes after US forces and the SDF stepped up their bombardment of Baghuz.
Once the village is taken, the US and its allies are expected to formally declare the end of the "caliphate" proclaimed by IS in 2014.
The group once controlled 88,000 sq km (34,000 sq miles) of territory stretching across Syria and neighbouring Iraq, imposed its brutal rule on almost eight million people, and generated billions of dollars from oil, extortion, robbery and kidnapping.
After five years of fierce battles, local forces backed by world powers have driven IS out of all but a few hundred square metres near Syria's border with Iraq.
Last Friday, the SDF said it had launched its final assault on Baghuz, declaring that nothing remained in the village "except for terrorists".
After a weekend of intense air and artillery strikes, the alliance said it had to slow down the offensive "due to a small number of civilians held as human shields".
SDF spokesman Mustafa Bali said about 3,000 people were evacuated on Monday and another 3,500, including 500 militants who surrendered, followed on Tuesday.
Five SDF fighters who had been held hostage by IS were also freed. But Mr Bali said the fate of other hostages - including the Italian priest Paolo Dall'Oglio and the Lebanese journalist Samir Kassab - remained unknown.
On Wednesday, a further 2,000 people left Baghuz, Reuters news agency reported. They were taken to an SDF checkpoint where they were searched, questioned and given food and water.
Some of the women evacuated were defiant despite the situation, chanting "God is greatest" and "Islamic State will remain" as they passed reporters on the front line.
The women and their children from Baghuz, including many foreigners who travelled to Syria and Iraq to live under IS rule, will be transported by lorry to an SDF-controlled camp called al-Hol.
A humanitarian organisation warned on Wednesday that the situation at the camp, where more than 50,000 people have arrived since December, was "completely overwhelming".
"Many of the arrivals are in a very weak condition or have life-changing injuries. Particularly vulnerable are the many heavily pregnant women as well as mothers with newborns," Misty Buswell of the International Rescue Committee said.
As of Monday, at least 90 people had died during the journey to al-Hol or shortly after reaching the camp, two-thirds of them babies and infants.
Many of the children do not have shoes or coats, while some families have had to sleep outside due to a lack of tents, exposing them to the cold and rain.