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The decision follows months of protests, with many saying that Marcos' record of corruption and rights abuses meant he should not be interred there.
Nine judges voted in favour of the burial, with five against the decision.
President Rodrigo Duterte had announced plans for the move shortly after his election in May.
In August, hegave the initial go-aheadfor the body to be buried in the National Heroes' Cemetery in Manila, calling Marcos a "Filipino soldier".
Critics had argued it was inappropriate to provide an honourable burial to a president blamed for thousands of killings, tortures and military abductions, many of which remain unresolved.
Marcos and his wife, Imelda, ruled the Philippines for 20 years before more than a million people took to the streets to overthrow them in what became known as the People Power Revolution of 1986.
His embalmed body is currently on display in his home city of Batac.
(BBC)
