The high court also recommended state prosecutors be investigated for bungling the case, the Philippine Daily Inquirer reported.
The government had filed the case in 1987 against Sen. Ferdinand "Bongbong" Marcos Jr., Ilocos Norte Gov. Imee Marcos and their sister, Irene Marcos-Araneta.
The Marcos family members were accused of using three media networks for their personal benefit, using an apparel company for dollar salting and illegally acquiring and operating a bus company.
The Supreme Court said in its decision government prosecutors had disregarded procedural rules and had not introduced in a trial court critical evidence the high court said would have proved the innocence or guilt of the Marcos siblings as alleged co-conspirators during the term of their father, who died in 1989.