There were chaotic scenes at stations across the capital after all trains stopped running on the RER A line, which cuts across the city, serving the Disneyland amusement park and La Défense business district and carriying 1.2 million people a day.
The strike began on Wednesday night when a passenger in Torcy, east of Paris, got his hand stuck in the closing doors and then head-butted the driver when he came to deal with the situation.
Drivers across the whole line then decided to go on strike in solidarity, demanding greater security, the first time the entire line has been shut down.
Secretary of State for Transport Alain Vidalies said he sympathised with the victim of the attack but that the strike "did not constitute the right response".
Trade unions, who had met management representatives on Thursday, said that it was up to drivers to decide whether they wished to return to work on Friday.
The lightning stoppage was a "spontaneous" action by drivers, unions say.
It was arguably in breach of French labour law, which requires public-sector unions to give notice of a strike five days beforehand and public transport workers to declare their intention of taking part 48 hours beforehand.
Drivers have linked their security concerns to pressure from management to keep to timetables that are difficult to respect on a line they claim has more traffic than it can handle.
The Paris region public transport company, the RATP, has promised to hold a meeting on Friday to try to tackle the staff’s grievances.