Ishihara, 66, defeated a host of contenders on Sunday. The outcome was a major defeat for Prime Minister Keizo Obuchi's ruling party, whose official candidate ended an embarrassing fourth.
Ishihara, author of the controversial book The Japan That Can Say No and a former transport minister, succeeds Tokyo Gov. Yukio Aoshima later this month. The governor-elect is also a vocal opponent of the U.S. military presence in Japan.
A clearly disappointed Obuchi said he was responsible for the outcome, which he called "very regrettable."
"I take it seriously," he was quoted as saying by Kyodo News service.
Although the head of Tokyo's municipal government has little influence over national policy, the governor's race was widely viewed as a political barometer for the country, as well as a gauge of Obuchi's popularity.
Reaction elsewhere in Asia was cautious.
In Seoul, the story was a major item in the international section of most nationwide newspapers. It made the front page of all the major newspapers in Taiwan.
Taiwan's Liberty Times, while welcoming Ishihara's support, urged Taiwan to distance itself from Ishihara's nationalism in order to maintain the delicate equilibrium between Taiwan, China, Japan and the United States.
Singapore's Straits Times offered a warning, saying, "His habit of upsetting China with outrageous statements and his hard-line stance against Japan's security alliance with the United States could prove embarrassing for the Obuchi administration in the future."
Ishihara interpreted his victory as a manifestation of the electorate's will.
"The people have waited for a strong and clear message," he told supporters in a victory speech.
Some expressed hope that the win would inject a dose of dynamism into the running of Japan's largest local government.
Ishihara, with his judgment and leadership abilities, could become Tokyo's answer to New York Mayor Rudolph Giuliani, the Nihon Keizai, Japan's top economic daily, said in an editorial Monday.
"Since Giuliani became mayor in 1993, New York became a clean and safer place to live," the paper said. "This showed a city's development depends on the leadership of its chief."
Others questioned Ishihara's lack of experience at the local level and his stubborn image.
"Saying `No' alone cannot push metropolitan politics forward," editorialized the nationally circulated Yomiuri newspaper, Japan's largest. "Coordination and leadership are needed to achieve policy."
Ishihara's campaign slogan was "The Tokyo that can say `No' to the country."
By Mari Yamaguchi