The 33-year-old timed 1hr 55min 36sec to come home more than a minute ahead of Britain's Georgia Taylor-Brown (1:56.50), with American Katie Zaferes (1:57.03) taking the bronze.
The upsets continued in the women's 400 medley when Japan's Ohashi delighted the host nation to topple defending champion Katinka Hosszu.
As China and Ecuador celebrated their wins, there was disappointment for Japan as gymnastics star Kohei Uchimura crashed out of the horizontal bar competition.
Just a few hundred officials and dignitaries were in the stands of the 68,000-seat venue to watch the spectacle which included Japan Emperor Naruhito declaring the Games open.
Algerian judoka Fethi Nourine says “we worked a lot to reach the Olympics... but the Palestinian cause is bigger than all of this.”
Planned initially for summer 2020, the Tokyo Olympics were held back by closed borders, and now a late resurgence in the virus means they will be played without any live spectators, either from Japan or abroad, according to an IOC ruling.
Tokyo 2020 President Seiko Hashimoto says that Kentaro Kobayashi has been fired as the Summer Games finally get underway.
Tokyo 2020 Olympics kicks off in empty venues to minimise health risks as WHO chief says Games should go ahead to demonstrate to the world what can be achieved with the right plan and measures.
Organisers insist games can go ahead with “proper measures” but a prominent public health expert warns “bubble system is kind of broken” and infections can spread to the local community.
The build-up to Friday's opening ceremony has been exceptionally rocky, with Tokyo still under a state of emergency and public opinion consistently against the Games, which will be held largely without spectators.
Two more athletes are reported to have tested positive on Monday as fears grow some games could be at risk.
The sentence is the first handed down in Japan in the Nissan saga, which began with former auto tycoon Carlos Ghosn's shock arrest in Japan in 2018 on financial misconduct allegations.
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