Interior Minister Manuel Valls appealed to the Council of State to intervene minutes after a judge in the city of Nantes overturned the ban.
Dieudonne M’bala M’bala has seven convictions for anti-Semitic hate speech.
He has already arrived at the theatre in Nantes, where more than 5,000 people were due to see the show.
Police have deployed outside the venue as a precaution. The verdict was greeted with boos and chants of Dieudonne M’bala M’bala’s name by those who had gathered to see the show.
On his Facebook page, Dieudonne M’bala M’bala appealed to those gathered outside Nantes’ Zenith theatre to return peacefully to their homes, saying he had been denied permission to address them.
The comic said that on Friday he would post a new video on his YouTube channel.
The judge in Nantes had earlier said he did not regard the show, entitled The Wall, as having “an attack on human dignity as its main object”.
But the Council of State upheld the ban on Thursday’s performance, the first on a scheduled tour, despite a challenge by the comic’s lawyers saying his freedom of expression had been breached.
The council cited the risk to public order in its reinstatement of the ban.
The president of the World Jewish Congress, Ronald Lauder, had called on France to “confront this preacher of hate head on”.
The government can be satisfied that a man they regard as a dangerous anti-Semite has been kept from the public arena.
Dieudonne M’bala M’bala’s supporters will say it is just more evidence of how he and his ideas are silenced by the system, he adds.
French media who have sent reporters to previous performances of The Wall say it contained a string of derogatory references to Jews.
Speaking on Thursday from Brittany, Manuel Valls said that “peddlers of hate stop at nothing and show boundless creativity”.
“Faced with this creativity of hate, should we do nothing? Certainly not. The status quo is not a solution,” he said.
The French government made a concerted effort to stop the tour after Dieudonne M’bala M’bala was recorded making remarks about Jewish journalist Patrick Cohen.
“When I hear him talking, I say to myself: Patrick Cohen, hmm… the gas chambers… what a shame,” he was recorded as saying.
He has also been accused of deriding Holocaust survivors and victims in his material.
On Monday, Manuel Valls said he had advised city mayors and police prefects that Dieudonne M’bala M’bala’s show could be banned if it was deemed to present a threat to public order.
However, Dieudonne M’bala M’bala’s lawyer said banning the show would be a clear breach of the principle of free expression, and that contrary to government claims, there was no evidence that his performances were a threat to public order.
The comic remains booked to play at a series of French venues until June, although the cities of Bordeaux and Marseille have cancelled his performances and in light of the latest ruling, it is not clear whether the rest of the tour can go ahead.
Dieudonne M’bala M’bala denies his trademark quenelle gesture is an inverted Nazi salute, instead describing it as an anti-establishment sign.
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