Backed by Abe's ruling coalition, Yoichi Masuzoe -- a former television pundit and one-time cabinet minister -- was an easy winner Sunday ahead of 15 rivals, including a former premier campaigning for an end to atomic power.
"It was good to see Mr. Masuzoe elected as he won support of people in Tokyo," Abe told reporters.
"I want him to work hard on various subjects such as low birth rate and longevity as well as economic revitalisation," Abe said. "I want him to make Tokyo a city shining at the centre of the world."
Chief Cabinet Secretary Yoshihide Suga separately told reporters: "I hope he will move the metropolitan government forward by cooperating with the Abe administration."
The poll for chief executive of one of the world's biggest cities had been seen as a referendum on atomic power in a country still scarred by the 2011 Fukushima disaster.
But livelihood issues appeared to play a bigger role in the election where voter turnout was put at 46 percent, the third lowest, on a weekend that had seen the Japanese capital hit with its heaviest snow in nearly half a century.
Masuzoe's win will provide a bounce for Abe and strengthen his hand on nuclear matters, observers say.
Like Abe, he has said that Japan needs to switch its reactors back on. All of them are idled at present amid public nervousness in the aftermath of the crisis at Fukushima.
Opinion polls show a significant number of Japanese oppose nuclear power, but the two main anti-atomic candidates never managed to shift the debate sufficiently away from the bread-and-butter issues that were the focus of Masuzoe's campaign, like the economy and welfare.
"While people are backing a gradual contraction of nuclear energy, they regard an immediate move to zero nuclear as not practical," said Koji Nakakita, professor of Japanese politics at Hitotsubashi University in Tokyo.
"The election result will be a boost for the Abe administration for sure," Nakakita added.
Between 2007 and 2009 Masuzoe served as health, labour and welfare minister, initially under Abe's first short-lived, administration.
The governor of Tokyo presides over Japan's most populated and wealthiest prefecture with a population of 13 million. Its annual 13-trillion-yen ($130 billion) budget rivals that of Sweden and it has 165,000 people on its payroll.
Masuzoe's in-tray will be filled with preparations for the 2020 Olympics, huge construction projects and the renovation of the city's ageing infrastructure already under way.
"I have to work with a sense of the heavy responsibility the post brings," Masuzoe told reporters. "There is no time to spare for relishing the result," he added.
Masuzoe, who will formally take office on Wednesday, is scheduled to visit Sochi to monitor the Winter Olympics as part of his preparation for hosting the Games as the head of the capital.