Voting was under way with no major hitches despite being held a day after the heaviest snowfall in 45 years. Observers say it may affect voter turnout in the city of 13 million people.
A crowded field of 16 men fought an uninspiring two-week campaign to become chief executive of one of the world's biggest cities.
Media surveys suggest one-time television presenter and former cabinet minister Yoichi Masuzoe has a commanding lead, despite his alignment with the government on the need to restart Japan's idled nuclear reactors.
The Japanese public has become increasingly sceptical of the once-trusted technology since the tsunami-sparked disaster at Fukushima in March 2011.
Separate polls by the Asahi Shimbun and Mainichi Shimbun have consistently given 65-year-old Masuzoe a comfortable lead over his closest rival, former prime minister Morihiro Hosokawa, 76, and renowned lawyer Kenji Utsunomiya, 67.
Both men have campaigned on an anti-nuclear platform and a win by Hosokawa, who has the backing of popular former prime minister Junichiro Koizumi, would create friction for the national government in its eventual aim to get nuclear reactors working again.
Most Japanese voters are against nuclear power, but the issue did not materialise in the national polls of December 2012 that swept pro-nuclear Shinzo Abe into the prime minister's office, with his opponents' apparent haplessness neutralising their anti-nuclear stance.
Economy, social welfare key issues
While policy-makers are looking at the Tokyo polls as a litmus test on the nuclear issue, much of the voting will come down to bread and butter issues such as the economy and social welfare programmes, pundits say.
A 72-year-old woman said she voted for Masuzoe as he appeared to care more about issues affecting the elderly.
"It's scarey to see the balance in my bankbook falling," she said as she came out of a polling station.
"I tried to resume working some time ago but was told (by a Tokyo city official) that it would deprive young people of jobs," the discontented pensioner told AFP.
Like the rest of Japan, Tokyo faces the question of how it should provide affordable care for the growing number of elderly people, but it must balance that with maintaining its appeal to the younger generations who make it such a vibrant commercial and cultural hub.
Between 2007 and 2009 Masuzoe served as health, labour and welfare minister, initially under Abe's first, short-lived, administration. He now has the backing of the prime minister's conservative Liberal Democratic Party.
At the same polling station, a 47-year-old man said he voted for an anti-nuclear candidate.
Some people said nuclear issues should not be on the agenda for Tokyo as it has no nuclear power stations, he noted.
"But electricity generated in Fukushima had been used in Tokyo," said the man who only gave his surname Sato. "Tokyo can't be self-sufficient in power supply. Could we afford not to think about the nuclear issue?"
Polling stations close at 8:00 pm (1100 GMT), with media exit polls expected shortly thereafter.
The post of Tokyo governor fell vacant in December when Naoki Inose stepped down after admitting he had been naive to accept an undeclared $500,000 from a hospital tycoon.
The office holder presides over Japan's most populated and wealthiest prefecture, where the local government's annual 13-trillion-yen ($130 billion) budget rivals that of Sweden and keeps 165,000 people on its payroll.
The new governor will likely spend much of his time preparing for the 2020 Olympics, with huge construction projects and the renovation of the city's ageing infrastructure already under way.