The result of the votes for president and vice presidents and other national leaders is expected to be officially announced Thursday, the anniversary of the US -backed Bay of Pigs invasion defeated by Cuban forces in 1961. His departure from the presidency is nonetheless a symbolically charged moment for a country accustomed to 60 years of absolute rule first by revolutionary leader Fidel Castro and, for the last decade, his younger brother.
Congress will select leaders of the legislature before choosing the president and other members of the Council of State, Cuba's top government body.
Fidel Castro was prime minister and president from 1959 until he fell ill in 2006.
Diaz-Canel smiled and joined the applause of the president. Although Osvaldo Dorticos was president of Cuba during Fidel Castro's time as prime minister, he was considered a figurehead beside the man who led Cuba's revolution, forged its single-party socialist system and ruled by fiat.
The next president is likely to be cautious at first, seeking to consolidate support among conservatives despite a desire for faster development of an economy smaller than it was in 1985, when Cuba had the support of the Soviet Union. Fidel Castro died in 2016 aged 90.
On Wednesday, Castro wore a dark suit in place of military fatigues and sat near Diaz-Canel as an official read out the names of proposed leaders to the 604 legislators gathered at a wood-panelled convention centre in a quiet Havana suburb.
Shunning the long speeches his brother was famous for, Raul Castro kept his low-key style even as he reached a landmark agreement in 2014 with former U.S. President Barack Obama to restore diplomatic ties with the United States.
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Infrastructure is crumbling, foreign investment is lagging and any hope that Cubans may have pegged on a warmer relationship with the US has faltered as renewed tensions have emerged under President Donald Trump.
Nauert said the administration would like to see "a more free and democratic Cuba" but is "not overly optimistic".
The legislators then cast secret ballots and were expected to nearly unanimously support the slate.
But with the economy suffering from a crisis in allied Venezuela and relations with the United States strained anew under President Donald Trump, some Cubans are pessimistic about their lives improving and feel nervous about what is to come. The CCN proposed Salvador Valdes Mesa for the post of first vice-president.
"The new president will have to create a new political consensus, he won't inherit one", said Rafael Hernandez, editor of the magazine Temas, which is affiliated to the Culture Ministry but takes a reformist stance.
"That's never happened in Cuba", said Miguel Saavedra, who is protesting the election.
Raul Castro looks up during an event in celebration of the 50th anniversary of the assault of the presidential palace during the regime of Fulgencio Batista, in Havana, Cuba, March 13, 2007.