The leader, who was ousted and forced into exile in 1986, died in the US in 1989. He had been embalmed and on display in his home city of Batac.
His burial follows a decision by the Supreme Court to allow him to be moved to the cemetery.
There have been protests against honouring a man blamed for thousands of killings, tortures and abductions.
Former presidents and artists of national significance are among those buried in the cemetery, although most are former soldiers.
In August, President Rodrigo Duterte gave permission for the burial, calling Marcos a "Filipino soldier".
The court approved it in November and the body was moved to the cemetery without announcement on Friday, surprising opponents of the burial.
The private ceremony was described as "very simple" and "just a family affair" by Police Chief Superintendent Oscar Albayalde, who helped manage security for the event.
He said it was not a state funeral, although the late leader was given a 21-gun salute.
Activist Bonifacio Ilagan, who was tortured under Marcos, told the Associated Press news agency the former leader was being buried "like a thief in the night".
Marcos and his wife, Imelda, ruled the Philippines for 20 years, a large part of it under martial law, before more than a million people took to the streets to overthrow them in what became known as the People Power Revolution.
As well as official brutality, the pair are accused of widespread corruption and the theft of billions of dollars of state funds.
Despite this, the family returned to the Philippines and political life, portraying the former leader's reign as a period of security, order and grand construction projects.
His son, Ferdinand "Bong Bong" Marcos Jnr, came close to winning the vice-presidency in May's elections. He told the BBC his father's reputation had helped, not hindered his campaign.