The 72,000-seat stadium was not on the original shortlist of venues bidding to host matches but World Cup officials agreed to accept a late application from Yokohama and the Kanagawa Prefecture, of which it is the capital.
A total of 15 cities and prefectures are now under consideration with a decision about the successful cities expected early next year.
"While we note that the deadline is passed for applications to host matches at Rugby World Cup, we have decided to accept this bid because we want to ensure that the tournament is available to as many sports fans as possible around the country," Japan Rugby 2019 chief executive Akira Shimazu said in a statement.
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"Yokohama's bid will now be considered on its individual merits along with all the others."
The full list of bidders is: Sapporo City, Iwate Prefecture and Kamaishi City, Sendai City, Saitama Prefecture and Kumagaya City, Tokyo, Shizuoka Prefecture, Aichi Prefecture and Toyota City, Osaka Prefecture and Higashi Osaka City, Kyoto City, Kobe City, Fukuoka City, Oita Prefecture, Kumamoto Prefecture and Kumamoto City, Nagasaki Prefecture, Yokohama and Kanagawa Prefecture.
"The international stadium at Yokohama is a world-famous venue and iconic for millions of soccer fans who remember when it staged the FIFA World Cup final between Germany and Brazil in 2002," Rugby World Cup chairman Bernard Lapasset said.
"We are delighted that Yokohama and Kanagawa Prefecture have submitted this application as it further demonstrates how the local governments in every part of Japan are keen to host matches at Rugby World Cup 2019 and welcome the rugby world to their cities."
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