Raul Castro, 81, formally assumed the presidency in 2008 – two years after replacing his ailing brother Fidel.
The Communist assembly, whose members ran for office unopposed, also chose Miguel Diaz-Canel Bermudez as Raul Castro’s first vice-president.
Miguel Diaz-Canel, 52, is widely seen as Raul Castro’s successor.
On Sunday, 86-year-old Fidel Castro – who was in power for five decades – made a rare public appearance at the opening session of the assembly in the capital Havana.
The Castros have been running Cuba under a one-party system since the 1959 revolution, which ousted the US-backed dictatorship of Fulgencio Batista.
Addressing the assembly following his re-election on Sunday, Raul Castro said: “This will be my last term.”
He had earlier called for a two-term limit and age caps for political offices, including the presidency.
But it is the first time he publicly said he would be stepping aside in 2018.
During his years in power, Raul Castro eased some restrictions on personal freedoms by lifting bans on mobile phones and home computers, and abolished the need of citizens to buy expensive exit visas when travelling abroad as tourists.
However, in his speech, he stressed: “I was not chosen to be president to restore capitalism to Cuba. I was elected to defend, maintain and continue to perfect socialism, not destroy it.”
Cuba has struggled economically since the collapse of the Soviet Union in the 1991 and now relies heavily on the support of the left-wing government of Venezuela.
Havana’s relationship with the US remains hostile – the two countries have no diplomatic relations and a decades-long American economic blockade is still in effect.
Until his promotion, Miguel Diaz-Canel was one of the eight vice-presidents on the council of ministers.
An electrical engineer by training, he rose through the Communist party ranks in the provinces and at one time served as education minister.
He would succeed Raul Castro if he is unable to serve his second full term in office.
Earlier in the day Raul Castro’s arrival, together with Fidel, and was warmly greeted by more than 600 assembly members.
Foreign press was barred from the opening ceremony.
Before Sunday, Fidel Castro was last seen in public earlier this month. Correspondents say he appeared frail and stooped at the time.
Fidel Castro has given up all his official positions, except his post as the assembly’s deputy leader.
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