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, which saw an emphatic victory by Yoichi Masuzoe -- a former television pundit and one-time cabinet minister.
Only around a third of eligible voters cast their ballots, media reported, down about 10 percentage points on the last election.
"I want to make Tokyo the number one city of the world, in areas including disaster prevention, welfare and the economy," Masuzoe told reporters as the scale of his victory became apparent.
"And above all, I will make the 2020 Olympic and Paralympic Games successful."
Even if nuclear power was not a decisive election issue, Koichi Nakano, professor of political science at Tokyo's Sophia University, said Masuzoe's win would give Abe a fillip and strengthen his hand on nuclear matters.
The vote had been triggered by the resignation of the previous governor, a policy wonk who admitted to political naivite after accepting an undeclared 50 million yen (USD 500,000) from a scandal-mired hospital magnate.
None of the major political parties had fielded a candidate, but all had swung behind one of the bigger players. Abe's conservative Liberal Democratic Party backed Masuzoe even though he left the party a few years ago.
Like Abe, he has said that Japan needs to switch its nuclear reactors back on. All of them are idled at present amid public nervousness in a country badly scarred by the disaster at Fukushima.
Former prime minister Morihiro Hosokawa, 76, did not manage to connect with voters despite having the high-profile backing of popular ex-premier Junichiro Koizumi.
