Attendees clashed with police, setting fire to a car and throwing objects at officers attempting to shut the event down. At least three officers were injured.
Police broke up the three-day party that defied a nationwide curfew
Police trying to stop the event faced "fierce hostility from many partygoers", a statement from local authorities said.
But at 05:30 local time on Saturday the ravers began to accept the party was over and started to leave the two disused warehouse hangars, the local prefecture said.
Interior Minister Gérald Darmanin said on Twitter that trucks, sound equipment and generators were seized at the scene and an investigation has been opened.
More than 1,200 fines were issued for non-compliance with the curfew, not wearing a mask and attending an illegal gathering, Mr Darmanin said.
On Friday authorities said they had opened a sanitary cordon around the party and anyone leaving the event was urged to self-isolate for seven days.
One of the party-goers, who gave his name as Jo, told the AFP news agency that "very few had respected social distancing" at the event.
A number of people slept in their cars before returning to dance, Le Monde newspaper reports.
One reveller told Le Monde that the rave was "very well organised" with food stalls inside.
Another, who came with four friends from Finisterre in north-west France, told the newspaper that she had wanted
to "escape" for a few hours.
On Friday an interior ministry crisis meeting was held and all vehicle exits from the rave were blocked as police sought to shut down the party.
Police issued more than 200 fines
France introduced strict rules ahead of the New Year including a curfew from 20:00 until 06:00.
More than 100,000 police officers were deployed across the country to break up parties and enforce the curfew.
France has recorded more than 2.6 million coronavirus cases and 64,892 deaths since the pandemic began.
Some revellers said they were hoping to stay until Tuesday