Portugal got the other available place when Canada withdrew its bid after the second round of voting at the UN General Assembly in New York.
China, Britain, France, the US and Russia are the five permanent members.
The 15-seat Security Council is one of the most important UN organs and is charged with maintaining international peace and security.
Every year, five of the non-permanent members step down after completing two years, and other countries battle to fill the seats.
Candidates are chosen by region and the main contest was among Western allies.
Germany won in the first round of voting, and Portugal in the second after Canada’s withdrawal.
India, South Africa and Colombia all secured their places in the council in uncontested votes.
The BBC’s Barbara Plett at UN headquarters says it is almost impossible for temporary members to block measures on which the permanent five agree, but they can block matters that require consensus and can influence the dynamics among the five big powers.
Among recent calls for reform of UN institutions, there have been proposals to expand the number of permanent members.
Brazil, Germany, India and Japan have all argued that they should have a permanent seat on the council.
Source: BBC