14-year-old Reynaldo de Guzman has been laid to rest.
His remains were buried at Pasig Public Cemetery on Wednesday morning.
His body was placed inside an apartment-type tomb.
Security was tight during the funeral.
A dozen security operatives from the Witness Protection Program (WPP) of the Department of Justice were present.
They were guarding the boy's parents, Lina and Eddie Gabriel, who have been placed under WPP.
The couple said they were very certain that the person they were burying was their son.
The boy's corpse was found floating in a creek in Gapan, Nueva Ecija last week.
His face was covered with a packaging tape and his body bore about 30 stab wounds.
The Philippine National Police had said the body did not belong to De Guzman.
The police said DNA samples taken from the body did not match the DNAs of his parents.
De Guzman was the companion of University of the Philippines student Carl Arnaiz before he was slain by Caloocan cops.
The police claimed they killed Arnaiz in a shootout after he supposedly robbed a taxi driver.