Masuzoe wants less dependence on nuclear power in the long run, while his main rivals, former Prime Minister Morihiro Hosokawa and Kenji Utsunomiya, a former head of the Japan Federation of Bar Associations, favored an immediate end to nuclear power.
Utsunomiya won about 983,200 votes and Hosokawa about 956,000 votes against Masuzoe's approximately 2,112,000 votes, the Japan Times reported Monday.
All of Japan's 48 operable nuclear reactors remain offline, pending safety checks after the March 2011 Fukushima nuclear power plant disaster triggered by a massive earthquake and tsunami.
Prior to the Fukushima crisis, nuclear power provided nearly 30 percent of Japan's electricity
Japanese Prime Minister Shinzo Abe, who has called for restarting Japan's idled nuclear plants, had stumped for Masuzoe during the campaign.
But an editorial in the Times Monday warned the Abe administration against regarding the election outcome "as a green light for continuing its efforts to push for the restoration of nuclear power generation."
Instead, it said, the administration should remember "that even Masuzoe declared that a majority of people want to build a society not relying on nuclear power."
After the election, the editorial noted, Masuzoe said Tokyoites supported his call for gradually decreasing nuclear power generation, and he also expressed hope to increase the share of renewable energy in the electricity used by Tokyo to about 20 percent from the current 6 percent.
The biggest user of electricity among Japan's 47 prefectures, Tokyo consumes about 10 percent of the nation's electricity.
In a poll by Japan's Asahi Shimbun newspaper a week before the election, only 14 percent of those surveyed said nuclear power was the deciding issue of the election. Yet, in the same poll, 74 percent of respondents wanted nuclear reactors completely eliminated either immediately or in the near future, the Wall Street Journal reports.
"All in all, the main issue was not nuclear power for most Tokyo residents," Meiji Gakuin University Professor Tomoya Kaji was quoted as saying by the Japan Times Sunday. "The camps that were calling for phasing out nuclear power were not able to make the matter an important issue."
But Meiji University Professor Yasushi Aoyama told the Japanese newspaper there wasn't enough discussion on the issue of nuclear power in the election. If the candidates approached the issue more seriously, he said, they would have addressed not only the makeup of Tokyo's energy sources, but also how to deal with issues such as electricity prices and transmission.
"It was not good that the candidates didn't provide a viable path" to zero-nuclear dependence, Aoyama said.