The indictment accuses the former deputy head of Saudi Arabia's general intelligence, Ahmed al Asiri, and former royal court adviser Saud al Qahtani of instigating "premeditated murder with monstrous intent,” prosecutors had said in March.
Eighteen other defendants are also accused of having carried out the killing of Khashoggi, who had grown increasingly critical of Saudi Arabia's de facto ruler Crown Prince Mohammed bin Salman (MBS). All 20 defendants are expected to be tried in absentia.
Khashoggi, a 59-year-old Washington Post columnist, was last seen at the Saudi consulate in Istanbul on October 2, 2018, after he entered there to seek documents for his impending wedding.
Turkish officials say his body was dismembered at the consulate by the killers and his remains are yet to be found.
"I hope this criminal case in Turkey brings to light the whereabouts of Jamal's body (and) the evidence against the killers," his fiancee Hatice Cengiz said.
A Saudi court sentenced five people to death and three to jail for the killing after a secretive trial last December.
Khashoggi's family later said they forgave his murderers, but Cengiz said neither the trial nor the pardon followed due process.
"No one can take the 'trial' that took place in Saudi Arabia legitimately; it was done in secret and the individuals sentenced are unnamed," she said.
Turkey has accused Saudi officials of obstructing investigations, while Riyadh repeatedly said Turkish prosecutor has not complied with requests to share information.
MBS has denied ordering the killing but said he bore ultimate responsibility as the kingdom’s de facto leader. Saudi Arabia initially denied any involvement in or knowledge of Khashoggi’s death but later changed its position several times.