Trump touched off global confusion and panic when he announced via tweet in mid-December that he would order the withdrawal of the 2000 troops stationed in Syria to help fight Isis - a move that both allies and critics warned could upset the balance of power in the Middle East, emboldening Russia and Iran, and threaten what tenuous stability US-aligned forces had been able to achieve in Syria.
Bolton's comments come amid reports that Trump had agreed to extend his initial 30-day deadline for withdrawal to four months.
When asked whether Bolton's comments would affect that timeline, a senior Administration official said that "there is no specific timeline for the withdrawal of US troops from Syria, and reports to the contrary are false".
Nonetheless, the plans and assurances the national security adviser offered in Israel were confirmation that withdrawal plans are slowing until conditions on the ground match the President's stated assessment of the situation in Syria.
As part of his announcement, Trump said the US had "defeated Isis" there - a claim that his advisers and political allies have disputed.
Trump's advisers and GOP allies have warned that pulling out US troops would also leave Kurdish fighters - who had been vital allies - susceptible to attacks by Turkey, where leaders see the group as a threat to their nation's sovereignty.
In a news conference with Israeli Prime Minister Benjamin Netanyahu, Bolton said that "the defence of Israel and other friends in the region is absolutely assured" and that the US would "take care of those who have fought with us against Isis and other terrorist groups".
He also said that the withdrawal would take place but "in a way to make sure Isis is defeated and is not able to revive itself and become a threat again".
But while Bolton's comments may have come as a relief to some, a top House Democrat stressed that the priorities the national security adviser outlined were "obvious" - and simply highlighted how dangerous Trump's initial withdrawal announcement was.
"We don't want Isis to rise again and be a transnational terrorist threat, and we don't want our allies the Kurds to be slaughtered by Erdogan in Turkey. That was obvious," House Armed Services Committee Chairman Adam Smith said on ABC. He was referring to Turkey's President, Recep Tayyip Erdogan.
Smith added: "I'm pleased that John Bolton has recognised the national security interest, and that's what we want to have ... not a tweet going 'Eh, let's get out of Syria'."
Smith said he hoped to have Mattis testify before his panel, calling the former defence secretary's views "invaluable".
In his resignation letter, Mattis noted disagreements he'd had with Trump over the President's approach to US allies and adversaries, and stated that Trump deserved a defence secretary whose views would be more aligned with his. Smith was more succinct in his assessment of Trump's approach to global relations, saying that "our allies matter enormously and the President treats them like dirt".
Democrats have lamented the departure of figures such as Mattis, whom they viewed as a tempering influence on Trump, and they worry about who will ultimately succeed them.
"All of the adults are one by one being forced out of the room," House Intelligence Committee Chairman Adam Schiff said on CNN. "Anyone who had the standing or the independence to speak out ... has been pushed aside and now you have a lot of yes-people serving the President."
Republicans, too, have worried about whether the President is listening to his advisers, warning him that the Administration's actions in Syria will affect America's reputation globally. At the time of Trump's announcement, some wondered openly whether he had simply agreed to get out of Syria to please foreign leaders whom the US has traditionally regarded more warily, including Erdogan.
Similar questions arose last week, after Trump offered a perplexing take on world history, incorrectly claiming that the Soviet Union's demise was a result of the Red Army's war in Afghanistan, which they apparently were forced to invade to address terrorist threats.
Schiff accused Trump of parroting "a Kremlin talking point" on Afghanistan.
