The bill will now proceed to the US House of Representatives for debate and another vote later tonight.
In late January, US lawmakers and Trump temporarily reopened the federal government for a three-week period until 15 February to negotiate a deal on border security. The main point of disagreement has been the Democrats' refusal to satisfy Trump’s request for $5.7 billion to build a wall on the US border with Mexico, which led to a record 35-day government shutdown.
Failure to enact the bipartisan security bill could shutter many federal projects, from air traffic controller training programs to the collection and publication of important data for financial markets, for the second time this year.
Trump has noted that congressional funding to construct a southern border wall continues to be the root of his dispute with Democrats.
"We need a wall [but] they do not want to give us a space to detain murderers, criminals, drug dealers", Trump said Monday.
Neither Trump nor his Democratic opponents in Congress appear ready to yield ground to end the dispute.
Earlier on Thursday, the White House confirmed Trump will use his executive authority to declare a national emergency in order to secure border wall funding. House Speaker Nancy Pelosi told reporters later on Thursday that Democrats would review their options and be prepared to respond appropriately.