The law firms representing dos Santos' daughter Tchizé dos Santos had earlier successfully requested a full autopsy citing alleged "suspicious circumstances" of his death, without providing evidence, and asked for his body to be buried in Barcelona.
The court ruling said the autopsy's final report had determined that dos Santos died of natural causes mainly triggered by a respiratory problem.
Dos Santos, who stepped down five years ago, died on July 8 at the age of 79 at a clinic in Barcelona, where he was being treated following a prolonged illness.
The court also said dos Santos had not indicated his desired burial place in his will, citing similar legal precedents to explain the judge's decision to hand the body to his widow Ana Paula Cristovao dos Santos and allow its repatriation.
The lawyers said they would appeal, arguing the judge is not competent to rule on the case as there is a separate legal process related to dos Santos' death.
A spokesperson for Catalonia's regional court system said the repatriation process would be suspended only if a judge accepts the appeal, adding that it was unclear how long it would take to process the appeal.
Tchizé and her lawyers have argued that dos Santos' wish was to be buried in Barcelona rather than his body being returned to Angola for a state funeral, which they say dos Santos's successor Joao Lourenço will likely use for political purposes.
Angola holds presidential elections on Wednesday, August 24.
Although handpicked by dos Santos, Lourenço swiftly moved to investigate allegations of multi-billion dollar corruption during the former president's era, often involving the dos Santos family. Dos Santos never specifically responded to the allegations that he had allowed corruption to become rampant.