Utsunomiya has pledged to reinforce the capital's medical services that buckled under the weight of the coronavirus crisis, while stressing the importance of offering more support to society's most vulnerable.
Tokyo confirmed 107 new coronavirus infections on Thursday, its highest daily tally in two months, but Japan's chief cabinet secretary said there was no need to reintroduce a state of emergency.
"The most pressing task is coronavirus measures, " she said.
Koike's victory was expected, with a recent poll by the Mainichi newspaper having her leading her opponents by a wide margin.
In a recent interview with AFP, Koike said she was continuing to "make all-out efforts in the battle against the virus to put on a Games that is full of hope".
The latest figure is set to fuel concerns about a second wave of infections in the capital, where business and social activities have been returning to normal in stages. "I say no to anyone who is against the Olympics, " he said. "I don't think they have a clear grasp of the current situation", he said, adding that he voted for Utsunomiya, who is pushing for more testing.
She has promised to ensure Tokyo's economic strength along with effective coronavirus measures, including the establishment of a disease control center in the metropolitan area.
Koike - who is running as an independent but with considerable support among those aligned with the ruling Liberal Democratic Party and its coalition partner Komeito as well as unaffiliated voters, according to polls - has vowed that Tokyo will host the games next summer in a simplified and safe form at reduced cost.
Japanese Prime Minister Shinzo Abe speaks at a news conference at the prime minister's official residence in Tokyo, Japan, June 18, 2020.
As the pandemic deepened in the spring, Koike often upstaged fellow conservative Abe, whose support ratings have plunged due to his handling of the crisis and its severe impact on the economy, on top of a slew of scandals.
A former TV newscaster and translator who also speaks Arabic and English, Koike earned the nickname "Migratory Bird" for hopping between parties and forming new alliances, a rarity among Japanese politicians who usually remain loyal to their party faction.