The incident, which was caught on camera and widely shared on social media, occurred on Wednesday on the sidelines of a rare demonstration by French police against "anti-cop hatred".
The footage shows a small group of masked protesters hammering the police vehicle with iron bars, smashing its windows before hurling in an explosive device that quickly fills the car with smoke and engulfs it in flames.
The policeman and policewoman inside were able to escape unharmed.
They are also accused of carrying out an armed attack against public officers, destroying public property and of participating in an armed group.
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"Investigations are continuing to determine their exact roles in the incident, and whether any other possible suspects should be arrested," the prosecutor's office in Paris said after the charges were read out by an investigating judge.
Prime Minister Manuel Valls earlier this week strongly condemned the police car attack, saying the punishment "must be harsh".
Much of the unrest has been blamed on small groups of troublemakers who appear bent on targeting the security services.
Over the past two months, some 350 members of the security forces have been injured during protests against the proposed labour reforms, which were forced through the lower house of parliament last week without a vote.