The closure of the plant on the border with Germany is part of a policy shift to reduce France's dependence on nuclear power.
The closure of France's oldest nuclear plant was mourned by electricity workers and celebrated by anti-nuclear campaigners on Monday.
The second of two 900-megawatt reactors at Fessenheim was being powered down and taken offline overnight. The first reactor was shut down in February.
The closure of the plant on the border with Germany is part of a policy shift to reduce France's dependence on nuclear power.
Germany has long called for the plant to be shut down.
Workers at electricity giant EDF, which operates Fessenheim and France's 18 other nuclear plants, described the closure as a tough blow.
However, it has been celebrated as a victory by anti-nuclear campaigners.
Andre Hatz, president of the "Stop Fessenheim" Association said he was happy the 50-year-long battle to get the plant closed had come to an end but he was concerned about what was being left behind.
He said: "(I'm) happy because of the permanent closure of the nuclear power plant, worried about the combustibles that will still be there for three years, in pools that are not bunkered without a safety system in place, and that would be really necessary".
Fessenheim's closure still leaves France with 56 pressurised water reactors at 18 plants. Nuclear energy supplies France with almost three-quarters of its electricity, more than any other country.
Under an energy strategy laid out in 2018 by President Emmanuel Macron, that balance is now shifting, with greater emphasis on renewables.
The government has outlined plans for 12 more reactor closures and for only half of France's electricity to still come from nuclear by 2035.