The bill, approved in a 316-90 vote by the US House of Representatives, had ignited criticism of Trump from some conservative members of Congress.
But it was passed by the Senate on Thursday and now goes to the Republican president, who is expected to sign it quickly.
Despite controversy, lawmakers had rushed to approve the legislation, which provides $15.25bn for emergency disaster aid, before government aid ran out at week’s end as Americans deal with two deadly hurricanes including Irma, a potentially catastrophic storm poised to strike Florida tomorrow.
Hurricane Harvey, which came ashore on August 25 as the most powerful hurricane to hit Texas in more than 50 years, killed about 60, displaced more than 1mn and the state governor has said it caused up to $180bn in damage.
The bill raised questions about the relationship between Trump, a political outsider who took office in January, and Republican Party regulars.
He has frequently criticised Senate leader Mitch McConnell and House Speaker Paul Ryan and his deal on Wednesday with Democratic congressional leaders Senator Chuck Schumer and Representative Nancy Pelosi was an especially troublesome shock for conservative members.
Conservatives’ souring relations with the administration are likely to remain a factor as Congress and the White House now face a December 8 deadline on the debt limit and government spending.
Asked about Trump working so closely with Democrats on the legislation, White House press secretary Sarah Sanders said: “I think that the president’s focus was doing what was best for the American people. I think the last thing we want to do is play partisan politics when we have people in places like Texas and Louisiana that need financial support through the federal government.”
Before the vote, US Treasury Secretary Steven Mnuchin and White House budget director Mick Mulvaney had pleaded the White House’s case to Republican lawmakers at a morning meeting yesterday.
It was not well received by some.
“There’s a lot of disappointment in the decision the president made and the way our leadership was treated,” said House Republican Representative Hal Rogers, describing a sense of “animosity” at the meeting. “That’s a sore spot. It’s not a happy camp.”
“There was some hissing and I don’t know if there was some booing but there were some groans,” Republican Representative Mark Walker said.
Mulvaney told the representatives that now was not the time to discuss Washington fiscal problems because of the hurricanes.
Conservatives reminded him that during his days as one of the most conservative members of Congress, he had been a strong advocate for threatening government shutdowns in order to win concessions on spending.
“It got a little warm for him a few times,” Walker said.
Moderate Republicans welcomed the bipartisan approach.
“If we can reach across the aisle, we can get things done and not be held hostage by 30 or 40 people,” said Representative Peter King. “You can’t just have one party govern.”
The bill’s $15.25bn in emergency funding includes $7.4bn for the Disaster Relief Fund at the Federal Emergency Management Agency (FEMA), $450mn for the Small Business Administration’s disaster loan programme, and $7.4bn for the Community Development Block Grant programme at the Department of Housing and Urban Development.
Some conservative groups had objected to coupling a debt-limit increase with the emergency funds but McConnell moved ahead at Trump’s urging.
Walker said Mnuchin gave conservatives little hope that the administration would fight to include the spending restrictions they want in the next debt ceiling increase in December.
In Wednesday’s meeting with congressional leaders, Trump had sought to work out a deal to attach to the disaster funding two short-term, three-month measures to fund the federal government at current levels and extended its borrowing limit, known as the debt ceiling.
Current government funding was set to expire at the end of the month, with a government shutdown looming, and the US Treasury had asked Congress to raise the debt limit immediately.
Some House Republicans balked at attaching the two crucial fiscal measures to the bill and called it a win for Democrats.
Republicans had wanted to raise the debt ceiling for a longer period that would have extended past the 2018 mid-term elections.
Republican Senator Ben Sasse said on Thursday that the deal makes Schumer “the most powerful man in America for the month of December”.
The three-month term of the debt limit and spending deal could give Democrats a better chance of winning higher government spending levels in December.
Republicans fear that having to deal with spending and debt again so soon will distract them from other issues, such as tax reform.