Officials in the Istanbul prosecutor's office confirmed to ABC News that the wanted men, royal court adviser Saud al-Qahtani and deputy intelligence chief Ahmed al-Assiri, are accused of planning and overseeing the killing of Khashoggi, which took place in the Saudi Arabian consulate building in Istanbul on Oct. 2.
Saudi officials say the men acted on their own authority and did not receive instructions from bin Salman to murder Khashoggi, a Saudi dissident with legal residency in the United States.
The arrest application filed in Turkish courts asserted there is "strong suspicion" the two aides were involved in planning the killing, officials confirmed to ABC News.
Turkey has been seeking to extradite 18 suspects, including 15 members of the alleged assassination squad. Saudi Arabia has detained 21 people and says it is seeking the death penalty for five.
Meanwhile, United Nations High Commissioner for Human Rights, Michelle Bachelet, described the killing as "awful" and has called for an international criminal investigation.
Bachelet was speaking at a news conference Wednesday timed for the 70th anniversary of the Universal Declaration of Human Rights.
"We also call for international investigation," she said. "We mentioned to the (U.N.) secretary-general that we thought it was needed, a criminal investigation — international investigation."
Although her office does not have the legal authority to initiate a criminal investigation, she said it would be a welcome step to determine "what really happened and who are the ones responsible for that awful killing."
The Turkish arrest warrants came one day after senior U.S. senators said they were more certain than ever that bin Salman was responsible for the killing, citing a CIA briefing.
"It's a complex issue, it's a shame, but it is what it is," Trump said. "It is America first to me, it is all about America first."