Khashoggi's body, which was dismembered, according to Turkish and Saudi officials, has not been found.
The Saudi Government belatedly acknowledged the involvement of its operatives but insisted they had disobeyed instructions to bring Khashoggi back to Saudi Arabia alive.
Even as Saudi officials have insisted that Mohammed - the kingdom's effective leader - knew nothing of the plot, the episode has led to greater scrutiny of his policies, including his decision to involve the Saudi military in a war in Yemen and his crackdown on domestic critics and rivals, including a group of prominent women's rights activists.
The Saudi Government has publicly reacted to the criticism with defiance - for example, condemning a recent US Senate resolution that blamed the Crown Prince for Khashoggi's killing. But Saudi officials have privately signalled their concern about the international fallout. Some had predicted that the response would include a government shake-up that might provide more seasoned counsel to the 33-year-old Crown Prince.
Yet the changes did not challenge Mohammed's nearly absolute control of the kingdom's foreign and domestic policy, and he retained his powerful post as defence minister.
Assaf has served as finance minister, a member of the board of Saudi Aramco, the state oil company, and as a governor of the International Monetary Fund.
He was also detained for several months last year during a round-up of hundreds of business executives, princes and government ministers in what Saudi authorities called an "anti-corruption" sweep.
Musaed al-Aiban, a longtime government minister who most recently headed a national cybersecurity authority, was named national security adviser.
His appointment ended, for now, speculation that the post would be filled by Prince Khalid bin Salman, a younger brother of the Crown Prince who serves as the Saudi ambassador to the US and has faced criticism for his early denials about a Saudi role in Khashoggi's disappearance.
Another appointee, Prince Abdullah bin Bandar, a young royal seen as close to the Crown Prince, was named head of the Saudi National Guard, a powerful security agency whose role has been to protect the royal family.