The move is an effort by the government to lower carbon emissions caused by air travel.
Lawmakers in the National Assembly passed the measure to discard routes under two and a half hours on April 10.
The bill will now pass to the Senate, followed by a final vote in the lower house.
However, the aviation industry has criticised the move after one of the toughest years for the sector due to the coronavirus pandemic.
Industry Minister Agnes Pannier-Runacher told Europe 1 radio: “We know that aviation is a contributor of carbon dioxide and that because of climate change we must reduce emissions.
“Equally, we must support our companies and not let them fall by the wayside.”
Meanwhile, some climate campaigners say the rule doesn’t go far enough.
Advice given by the Citizens’ Climate Convention called for domestic flights to be abandoned in the event a train journey of fewer than 4 hours was possible along the same route.
"The four-hour limit would have made it possible to delete the routes that emit the most greenhouse gases," said Danièle Obono, of the La France Insoumise party.
The vote comes after the government announced it would double its stake in Air France-KLM, financing a €4bn (£3.5bn) recapitalisation to help the airline stay afloat after the pandemic left most of their flights grounded.
The domestic flight ban is part of a wider climate bill aimed at combatting France’s emissions, cutting them by 40 per cent of 1990 levels by 2030.
Other recent proposals voted on by MPs as part of the climate bill include the sale of ‘loose’ items in supermarkets in an effort to reduce the quantity of packaging.
The amendment, approved last Friday suggests that shops bigger than 400 sq metres will devote 20 per cent of their surface area to the sale of bulk items between now and 2030.
MPs also voted to improve labelling on products by including a “carbon score” to boost transparency on how and where the garments are made.