At least some of the civilians were later released or escaped, the alliance said on Saturday, but the whereabouts of the rest was unknown.
“There are no more IS fighters” left in Manbij, an SDF member said.
Kurdish television showed footage of jubilant civilians in Manbij, including smiling mothers who had shed their veils and women embracing Kurdish fighters.
A woman burned a black robe that the jihadists had forced residents to wear, while men who had lived for weeks under a shaving ban cut their beards with scissors.
“The battle was very hard,” a Kurdish source told AFP.
“And the jihadists had laid mines” in the city.
“One SDF fighter entered a house on Friday and saw a shoe placed on a Koran. When he removed it there was an explosion and he was killed,” this source said.
The Syrian Observatory for Human Rights, a British-based monitor, reported that several hundred of the civilians taken from the city were no longer being held by IS.
“Among the civilians taken by IS there were people used as human shields but also many who chose voluntarily to leave the town due to fear of reprisals” by the SDF, Observatory head Rami Abdel Rahman said.
The SDF launched an assault in May on Manbij, on a key jihadist supply route between the Turkish border and IS’s de facto Syrian capital Raqa.
The jihadists, who have suffered a string of losses in Syria and Iraq, have often staged mass abductions when they come under pressure to relinquish territory they hold.
IS has also booby-trapped cars and carried out suicide bombings to slow advances by their opponents.
SDF forces captured Manbij on August 6 but had continued to battle pockets of jihadists in parts of the town.
According to the Observatory, 437 civilians, including more than 100 children, were killed in the battle for Manbij and surrounding territory.
Around 300 SDF fighters died, along with more than 1,000 jihadists, it said.
Pentagon deputy press secretary Gordon Trowbridge said Friday that IS “is clearly on the ropes”.
“It has lost the centre of Manbij, it has lost control of Manbij,” he said.
Since fighting for Manbij began, US-led strikes have taken out more than 50 of IS’s heavy weapons and destroyed more than 600 fortified fighting positions, Trowbridge said.
But the job of clearing the city will be complicated after the jihadists left behind hundreds of mines and booby traps, he added.
Syria’s conflict erupted in March 2011 and has since killed more than 290,000 people and drawn in world powers on all sides of the war.
On Friday Russian and Syrian jets pounded rebel positions in and around second city Aleppo.
The raids came despite a pledge by Russia to observe a three-hour daily ceasefire in Aleppo to allow for humanitarian aid deliveries.