Switzerland, Mozambique, Malta and Ecuador will also take up two-year positions from January 1 next year.
The five will succeed India, Norway, Kenya, Mexico and Ireland.
The Council is made up of 15 members, five of whom are permanent: the United States, Russia, China, France and Britain.
The other ten positions are filled by other countries for two-year stints, five of which are announced each year.
Japan, Switzerland, Mozambique, Malta and Ecuador were voted in by the UN General Assembly in a secret ballot.
Out of the assembly's 193 members, Japan obtained 184 votes.
Deputy foreign minister Odawara Kiyoshi said Tokyo's priorities would be "security, including energy and food."
Mozambique was elected to the Council for the first time in its history with 192 votes.
Switzerland won 187, Malta 185 and Ecuador 190.