Prime Minister Jean Castex announced the measure on Friday night after an emergency government health security meeting at the presidential palace, warning of a "great risk" from the new variants.
All those arriving from other EU countries will be required to produce a negative Covid-19 test, he said.
France will also close all large shopping centres from Sunday and limit travel to and from its overseas territories.
Mr Castex ordered increased police checks of those who violate France's 12-hour-a-day curfew.
Many doctors have been urging a new nationwide shutdown like those imposed in several other European countries.
Mr Castex said the measures are an attempt to avoid the economic cost of a third lockdown.
France has reported more than 75,000 deaths, the seventh highest in the world.