Officials said the ashes were interred on Sunday, near those of national hero Jose Marti, Efe news agency reported.
Cuba President and Fidel's younger brother Raul Castro, placed the urn containing the former leader's ashes inside a stone -- that some reports said was brought to the cemetery from the Sierra Maestra Mountains -- where the revolution was launched in the 1950s.
The interment of Castro's ashes was reportedly attended only by relatives and special guests, including Venezuelan President Nicolas Maduro, Bolivian President Evo Morales and former Brazilian Presidents Luiz Inacio Lula da Silva and Dilma Rousseff.
Authorities kept the press and about 100 people, who gathered outside the cemetery's gates, out of the burial ground.
The vehicle transporting the ashes left the cemetery empty about two hours after arriving, and the guests invited to the ceremony left soon after.
Thousands of people lined the streets of Santiago de Cuba on Sunday, as the funeral cortege made its way to the cemetery, shouting slogans of "Yo soy Fidel!" (I Am Fidel!) as the ashes passed.
The late Cuban leader's ashes arrived in Santiago de Cuba from Havana on Saturday after a four-day journey covering nearly 1,000 km.
Castro, who had been out of office for a decade, died on November 25 at the age of 90 in Havana.