"He basically said that he was not personally responsible for it," Biden said of the crown prince's response during their meeting. "I indicated that I thought he was."
The president said they also discussed energy and that he expected to see "further steps" from Saudi Arabia, a major oil producer, on energy in the coming weeks.
As a presidential candidate, Biden had said the kingdom should be made a "pariah" on the world stage because of the murder. He said on Friday he did not regret that comment.
Energy and security interests prompted Biden and his aides to decide not to isolate the Gulf oil giant that has been strengthening ties with Russia and China.
The president's interaction with the crown prince drew criticism at home - beginning with the fist bump.
At the start of Biden's Middle East trip, officials said he would avoid close contacts, such as shaking hands, as a precaution against COVID-19. But the president ended up engaging in hand-shaking during the Israel leg of the tour.