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, he gave the initial go-ahead for the body to be buried in the National Heroes' Cemetery in Manila, calling Marcos a "Filipino soldier".
