He was found on Thursday morning and is said to have suffered from depression.
Popularly known as "Fidelito", he was the first-born son of the former president, who died in November 2016.
Castro Díaz-Balart worked as a nuclear physicist having trained in the former Soviet Union.
"Fidel Castro Diaz-Balart, who had been treated by a group of doctors for several months due to deep depression, took his life this morning," Cuba's official newspaper Granma reported.
State television said he had been receiving medical treatment as an outpatient in recent months, following a hospital stay.
At the time of his death, he was a scientific adviser for the Cuban Council of State and he served as vice president of Cuba's Academy of Sciences.
His professional profile says he authored several books during his life, and represented the country academically at international events around the world.
The television announcement said his funeral would be planned by his family, but no further details were given.
His father, Fidel Castro, a revolutionary figure and one of the world's longest serving political leaders, died at 90 in 2016.