The fall of Raqqa, where Isis staged euphoric parades after its string of lightning victories in 2014, is a potent symbol of the movement's collapsing fortunes. The city was used as a base for the group to plan attacks abroad.
The Syrian Democratic Forces (SDF), an alliance of Kurdish and Arab militias backed by a US-led international alliance, has been fighting Isis inside Raqqa since June.
SOHR said 3,250 people were killed in the five-month battle, including 1,130 civilians.
A witness said fighting appeared to be almost at an end with only sporadic bursts of gunfire.
Militia fighters celebrated in the streets, chanted slogans from their vehicles and raised a flag inside Raqqa stadium.
An SDF spokesman said the alliance would capture the last Isis areas in the city within hours.
Save The Children has warned that the humanitarian crisis in northeast Syria is "rapidly escalating", with 270,000 people who have fled the fighting in "critical need" of aid and camps "bursting at the seams".
On Saturday a deal was brokered for the last remaining local fighters in Raqqa to leave the city.
SDF spokesman Talal Silo said then that any fighters who were not signed up to the deal would be left behind "to surrender or die”.
The jihadists' last bases in the city, a stadium and a hospital, were captured earlier on Tuesday, the SDF said.
A local field commander said no Isis fighters remained at the two central points where militants had been best entrenched and where the SDF said fighting on Monday night and early Tuesday was focused.
"We do still know there are still IEDs and booby traps in and amongst the areas that ISIS once held, so the SDF will continue to clear deliberately through areas," said Colonel Ryan Dillon, a spokesman for the coalition.
In a sign that the four-month battle for Raqqa was in its last stages, Col Dillon said there had been no coalition air strikes there on Monday.
It is now hemmed in to a tiny bomb-cratered patch of the city around the stadium that was being pounded from the air by a US-led coalition and encircled by SDF fighters.
Isis has lost swathes of territory in Syria and Iraq this year, including its most prized possession, Mosul, and in Syria it has been forced back into a strip of the Euphrates valley and surrounding desert.
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