The other rebels either left the city or pledged allegiance to ISIS, the observatory said. That means the city is controlled partly by the government and partly by ISIS. Deir Ezzor is 100 kilometers (62 miles) east of the Iraqi border.
ISIS now controls about 95% of greater Deir Ezzor province, which borders Iraq, the observatory said.
In other violence over the weekend in Iraq, militants believed to be with ISIS attacked the city of Haditha from four directions, said Hameed Ahmed al-Hashim, a member of the Anbar provisional council, and two security officials in Haditha.
A large military force backed by tribesmen defended the city, they said.
Iraqi jet fighters bombed a bridge controlled by militants east of Falluja, causing structural damage, al-Hashim said.
Three police officers were wounded when a roadside bomb exploded near their convoy in Kirkuk, a security official told CNN on Saturday.