A court in Mamoudzou on Tuesday stopped the clearance of one slum located at Koungou near the capital at the last minute, saying the action had no legal foundation and threatened public liberties.
The local administration said it would appeal.
Locals feted the court decision stopping the evacuation, which was due early Tuesday.
"I am overjoyed, we went to court and we won," exulted Mdohoma Hadja, 33, raising her arms to the skies.
Comoros, whose three islands lie to the northwest of Mayotte, said Monday it had refused to allow a boat carrying migrants from the island. Most of the illegal migrants being deported are Comoran.
It also said it had suspended passenger traffic at a port where deported migrants usually land.
"We will not stop the operations... to fight against delinquency and unsanitary housing, with their consequences on illegal immigration," the most senior Paris-appointed official on Mayotte, Thierry Suquet, told reporters.
He said he hoped to "quickly resume" boat deportations to Anjouan and hoped the standoff would be resumed through "dialogue."
But Comoros' leader Azali Assoumani - who has held the rotating presidency of the African Union since February - said he hoped the operation would be abandoned, admitting Moroni didn't have "the means to stop the operation through force."
In 2019, France pledged 150 million euros ($161 million) in development aid as part of a deal to tackle human trafficking and ease the repatriation of Comorans from Mayotte.
Around half of Mayotte's roughly 350,000 population is estimated to be foreign, most of them Comoran.
Many African migrants, especially Comorans, try to reach Mayotte illegally every year.
These risky crossings risk ending in tragedy when the "kwassa kwassa" -- the small motorised fishing boats used by people smugglers -- are shipwrecked.
Mayotte is the fourth island of the Comoros archipelago that France held on to after an initial 1974 referendum, but it is still claimed by Moroni.
