The stencilled mural next to the emergency exit from which hundreds fled the massacre by jihadist gunman in 2015, is the eighth apparently created by the artist in the French capital in recent days.
Ninety people died inside the venue in the attack claimed the Islamic State group during a concert by the US group Eagles of Death Metal.
Some saw the piece as a poignant farewell to the city by the world's most famous graffiti artist, who earlier took aim at the French government's
crackdown on migrants in another more elaborate work close to a former refugee reception centre.
It shows a young black girl spraying a pink wallpaper pattern over a swastika on a wall next to her sleeping bag and teddy bear in an attempt to make her patch of pavement more cosy.
Eritrean refugees Ibrahim and Goitom, who have been sleeping next to the mural at Porte de la Chapelle in northern Paris, said they had never heard of Banksy.
After being told that the artist's work has sold for more than $1 million, Ibrahim — who said he could not remember when he had last slept in a bed — said that he would protect it.
Migrants sleeping by mural
“You can tell Mister Banksy that we will look after it. We will not let anyone touch it,” he told AFP Sunday.
“He is trying to help refugees. No many people want to help us.”
Nevertheless, part of the mural was sprayed with blue paint on Sunday night, covering the swastika and the girl's head and torso.
Fans of the artist started covering some of the other new works with Plexiglass on Monday to protect them.
Banksy, a long-time supporter of the refugee cause, has yet to confirm the works are his.
The refugee shelter known as “The Bubble” was controversially closed in March despite protests from the city's Socialist mayor Anne Hidalgo.
She hailed Banksy's intervention Monday. “Sometimes an image is worth a thousand words. Humanity and pragmatism rather than populism,” she tweeted in a dig at French President Emmanuel Macron, who had argued the shelter was making Paris a magnet for migrants.
The biggest of the new works in Paris shows Napoleon rearing his horse as he crosses the Alps to invade Italy in 1800, his face and body wrapped in his red cloak.
The pastiche of David's canvass, one of the most iconic in French 19th-century art, has been taken as a cutting take on France's ban on the niqab and other Islamic veils that cover the face.