As technicians closed down the No. 3 unit at Tomari in Hokkaido at 11:03 pm (1403 GMT), the debate over whether Japan needs nuclear power has been reignited, amid increasingly shrill warnings of summer power blackouts.
Hokkaido Electric Power, which runs the plant, suspended power generation for mandatory maintenance and is scheduled to bring the reactor to "cold shutdown" some time on Monday, said company spokesman Hisatoshi Kibayashi.
The shuttering marks the first time since the 1970s that resource-poor and energy-hungry Japan has been without nuclear power, a technology that had provided a third of its electricity until meltdowns at Fukushima.
The tsunami-sparked disaster forced tens of thousands of people from their homes in an area around the plant -- some of whom may never be allowed to return.
It did not directly claim any lives, but has devastated the local economy, leaving swathes of land unfarmable as radiation spewed from the ruins.
With the four reactors at Fukushima crippled by the natural disaster public suspicion of nuclear power grew, so much so that no reactor shut for routine safety checks has since been allowed to restart.
"A new era in Japan with no nuclear power has begun," said Gyoshu Otsu, a 56-year-old monk who joined a protest against nuclear power in front of the industry ministry in Tokyo which supervises the nation's power utilities.
"Generating nuclear power is like a criminal act as a lot of people are still suffering," said Otsu wearing white Buddhist clothes. "If we allow the situation as it is now, another accident will occur."
Protest organiser Masao Kimura said: "It's a symbolic day today. Now we can prove that we will be able to live without nuclear power."
Demonstrators stage rally
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 (Goodbye), nuclear power".
"We have to take action now so that Fukushima should be the last nuclear accident not only in Japan but all over the world," Mizuho Fukushima, head of the opposition Social Democratic Party, told AFP during the rally.
But Hiroomi Makino, the pro-nuclear mayor of Tomari, which hosts the reactor, said: "It's so regrettable. I would like the company to resume operation as I believe that they will give the highest priority to safety."
As the reactor shuts down, Japan's entire stable of 50 reactors will be offline, despite increasingly urgent calls from the power industry and bodies like the OECD, who fear dire consequences for the world's third largest economy.
Last month, Kansai Electric Power, which supplies mid-western Japan, including the commercial hubs of Osaka, Kyoto and Kobe, said a hot summer could see supply fall nearly 20 percent short of demand.
Kyushu Electric Power, covering an area further west, as well as Hokkaido Electric Power also said they will struggle as air conditioning gets cranked up in Japan's sweltering summer.
Kansai Electric last month booked a $3 billion annual loss, turning around a $1.5 billion profit the year earlier on the increased cost of using previously mothballed thermal fuel plants.
A week earlier, Prime Minister Yoshihiko Noda's government gave the green light to restarting reactors at the Oi nuclear plant, run by Kansai Electric, but regulators still have to convince those living near the plant.
In order to be fired up again, reactors must now pass International Atomic Energy Agency-approved stress tests and get the consent of their host communities -- it is this last hurdle that is proving hardest to overcome.
Goshi Hosono, state minister in charge of nuclear policy, told reporters: "Situations surrounding electric power are severe, but we can't sacrifice safety. We want to face the reality firmly."
Critics of nuclear power say Japan has managed thus far with its ever dwindling pool of reactors and need not look back.
Environmental campaign group Greenpeace said Friday the country should concentrate on ramping up renewables and boosting energy efficiency.