It is the first time in four decades that the island nation is not using nuclear reactors to generate any electricity.
Hokkaido Electric Power, which runs the plant, said it had started inserting control rods that will halt the chain reaction and bring the reactor to "cold shutdown" some time on May 7.
With the shutdown, Japan's entire stable of 50 reactors will be out of operation.
Thousands of antinuclear protesters marched in Tokyo to call for the government to permanently renounce nuclear power.
Some of the protesters gathered in front of the Industry Ministry in Tokyo, which supervises the nation's power utilities.
Protest organizer Masao Kimura said: "It's a symbolic day today. Now we can prove that we will be able to live without nuclear power."
Separately, some 5,500 demonstrators staged a rally at a park near Tokyo Tower and later marched through central Tokyo carrying banners, which read "Sayonara, nuclear power."
The shutdown of the last operating reactor comes as the Japanese government requires reactors to pass new tests to withstand earthquakes and tsunamis in the wake of last year's Fukushima disaster. To be restarted, they need local residents' approval.
However, in the wake of Fukushima, public suspicion of nuclear power has grown so much that no reactor shut for routine safety checks has yet received local approval to resume operation.
The Fukushima disaster forced tens of thousands of people from their homes in an area around the stricken plant, some of whom may never be allowed to return.
Japan usually uses nuclear power to generate one-third of its electricity.
Critics of nuclear power say Japan has managed thus far with its ever-dwindling pool of reactors and need not look back.
The government rejects that position, saying that nuclear energy is essential to assure the country has a diversity of power sources beyond imported oil and gas.