He insisted Saudi officials did not know the whereabouts of Mr Khashoggi’s remains.
On Friday, Saudi Arabia finally admitted its agents had killed Mr Khashoggi after he entered the consulate on 2 October.
It claimed he had died in a”fistfight”, that 18 Saudi suspects were in custody and intelligence officials had been fired.
But the kingdom denies its crown prince or king were involved.
Mr al-Jubeir echoed Donald Trump’s warnings about rushing to judgement against Saudi leaders, saying ”there is the presumption of innocence until proven guilty,” and that some have “turned that upside down”.
He extended his condolences to the family of the journalist, saying: ”We can feel their pain and we wish this didn’t happen and I wish that this could have been avoided.”
It comes as the Saudi crown prince, Mohammed bin Salman, and King Salman called Mr Khashoggi’s son to express their condolences, according to the state-run Saudi Press Agency.
Mr Trump has said he will talk to the crown prince ”very soon” before deciding what to do next.
He said he planned to consult with Congress to devise a response. “We’ll have an answer by probably Tuesday or so,” he said.
Mr Trump has repeatedly said over the last week that he opposes any effort to impede more than $100bn (£76.4bn) in US arms sales to Saudi Arabia, but that he would consider sanctions on the kingdom.
Asked if he believed the Saudi explanation that Mr Khashoggi was killed during a “fistfight” with more than a dozen agents was credible on Friday, he said: “I do. I do.”
But on Saturday, in an interview with The Washington Post, Mr Trump said: ”Obviously there’s been deception and there’s been lies.”
Britain, Germany and France have issued a joint statement saying “nothing can justify” the killing of Mr Khashoggi.
In a statement released on Sunday, the governments said there was an “urgent need for clarification of exactly what happened” and said attacks on journalists are unacceptable and “of utmost concern to our three nations”.
They said the “hypotheses” proposed so far in the Saudi investigation need to be backed by facts to be considered credible.