In a ruling that will increase the pressure on the video-sharing website to ban the comedian from its platform altogether, a judge ruled that one of the passages breached French law on Holocaust denial and another one amounted to incitement to racial hatred.
Dieudonne M'bala M'bala was given five days to remove the passages or face a penalty of €500 per day for each of them left online.
Stephane Lilti, a lawyer representing France's Union of Jewish Students (UEJF) which brought the legal action, said they would now ask public prosecutors to ensure that the court's ruling is enforced.
The UEJF said it would be approaching YouTube for talks over the steps the site should take to ensure that "they respect their legal obligations in future."
YouTube, which has already withdrawn one Dieudonne video after he was convicted over its content, would not comment on whether it would be pulling the video – "2014 Year of the Quenelle" – that was the subject of Wednesday's ruling.
In the passage deemed to constitute Holocaust denial, Dieudonne claims to "know nothing about the gas chambers" but says he can organize a meeting for anyone interested with "Robert" – which the court accepted was a reference to Robert Faurisson, a notorious former academic who claims the systematic massacres of Jews in World War II never happened.
"In the context of previous statements by Dieudonne, some of which have earned him convictions for hate speech, defamation and incitement to anti-Semitism, it seems clear that this reference amounts to disputing a crime against humanity," the judge, Marc Bailly, said in his ruling.
'Who who provoked whom, Jews or Nazis?'
In the second contested section, Dieudonne insists he is not anti-Semitic then goes on to say he shouldn't be required to judge between "the Jews and the Nazis."
"I don't know what happened, who provoked whom, who stole from whom," he adds before delivering the punchline: "I've got my little idea, but... you know."
Dieudonne's lawyers said these comments were clearly humorous but their argument was rejected by the judge who said any humor involved was being put at the service of Dieudonne's beliefs and desire to test the limits of free speech.
Thursday's court hearing was the latest battle in a war between Dieudonne and his supporters and opponents led by France's Socialist government.
The government succeeded in preventing Dieudonne from touring his latest show around the country but it has been unable to prevent him performing altogether and there is no sign of him becoming any less popular.
Last week, the 47-year-old was acquitted on charges related to another video in which he calls for the release of an Islamist militant serving life for the 2006 kidnap, torture and murder of French Jew Ilan Halimi.
The government has also targeted Dieudonne's finances.
Efforts to get him to pay more than €65,000 ($90,000) in outstanding fines for his race hate convictions have led to a probe into suspected money laundering and misuse of company assets by the comedian.
Dieudonne, who was banned from entering Britain last week, has long enjoyed cult popularity in France but he has been catapulted to another level of fame in recent months by the popularity of his "quenelle" - a stiff-armed pose that he defends as an anti-establishment gesture but critics see as a disguised Nazi salute.
Former France international footballer Nicolas Anelka is currently awaiting the outcome of disciplinary proceedings against him after he performed a quenelle goal celebration for his English club, West Brom, last month.