The four men were among 14 people on trial in connection with the terrorist assaults in January 2015, whose actual perpetrators were killed after jointly planning the attacks.
Paris Mayor Anne Hidalgo called the fine “obviously absurd, unfair, irresponsible and dangerous.”
Clashes erupted between police and pockets of protesters, most dressed in black and their faces covered.
"We have a first principle which is the highest respect for Islam," Le Drian told reporters. "I also want to say that Muslims are fully part of society in France."
The issue goes to the heart of the Republic and France’s attempt to maintain its traditions of freedom and secularism against a rising tide of religious extremist hate linked to Islamist intolerance.
Investigators were trying to establish whether the attacker, who was shot dead by police, had acted alone or had accomplices.
Rumors surrounding the attack suggest that the teacher had presented caricatures of Muhammad, which the attacker took as an incentive for the murder.
The curfews will take effect from Saturday, and will run daily from 9:00 pm (1900 GMT) until 6:00 am the following morning, Macron said in an interview broadcast on national television.
The specimen is unusual because it is so complete: around 70% of the bones are present, and they were found aligned with each other, making it easier to reconnect them during the restoration process.
A 31-year-old man was arrested at the scene and is suspected of spray-painting the 20 red swastikas on walls and columns in Place de la Concorde and Rue de Rivoli.