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Scheduled to take place on March 1, it is one of the biggest marathon events in the world. Over 37,000 people took to the start line of last year's event.
But after a number of cases of the virus were recorded in Tokyo, organizers said they cannot "launch the event within the scale we originally anticipated."
The virus has infected more than 71,000 people around the world with the current death toll standing at 1,775, including five people outside mainland China.
Registered runners are able to defer their entry to the 2021 event, but entrance fees will not be refunded.
Last week, Tokyo 2020 Olympics organizers said the Games remain "on track" to take place as planned despite the virus outbreak. They also said there were no contingency plans of canceling or moving the Games.
A number of sporting events in Asia have already been postponed, including the Chinese Grand Prix -- originally scheduled for April 19 -- and the Hong Kong and Singapore Sevens tournaments, which have been moved from April to October.