Yoichi Masuzoe, a former cabinet minister, took more than 30 per cent of the vote, according to a television exit poll, to win by a comfortable margin over 15 other candidates. Masuzoe, who was backed by Japan's conservative ruling party, will take office almost exactly three years after the worst nuclear disaster in decades took place in Fukushima, about 150 miles north of Tokyo.
The election was regarded as a test of public support for nuclear power. Both of Mr Masuzoe's two main rivals were strongly anti-nuclear.
As his victory became apparent, Masuzoe, 65, told journalists: "I want to make Tokyo the number one city in the world."
Experts described Masuzoe's win as a boost for the pro-nuclear prime minister, Shinzo Abe, as the government prepares to restart Japan's nuclear power stations, all of which were shut down after Fukushima. However, the election happened after a heavy snowfall and the turnout was low, with only a third of voters participating.
The role of Tokyo's governor - the equivalent of mayor - involves running the nation's wealthiest and most populated prefecture, with 13 million people and a budget of pounds 79 billion.
Masuzoe will face a string of challenges in addition to the future of nuclear energy. Topping his agenda will be the 2020 Olympics, with major infrastructure projects already under way. He must also try to win over the capital's female population. In 1989, Mr Masuzoe told a men's magazine that menstruation made women unfit for government. Before the election, thousands of women joined a Twitter campaign threatening a "sex strike" against any man who voted for Masuzoe.