The so-called "minibus" appropriations bill includes nearly $675 billion in spending for the Department of Defense, as well as about $182 billion for an array of domestic programs under the departments of Labor, Health and Human Services, Education and related agencies.
Congressional aides said the Senate combined the two bills in the hope that President Donald Trump would not veto the domestic spending measure.
Trump has threatened to shut down the government if Congress, which is controlled by his fellow Republicans, does not adhere to his spending priorities, especially his desire to spend billions of dollars to build a wall on the border with Mexico.
On Wednesday, his administration announced its position on the bill. While not threatening a veto, the "Statement of Administration Policy" noted that the bill does not include administration proposals to reduce spending in areas such as education and healthcare research.
It also balks at some defense spending reductions, including a $532 million reduction in Afghanistan security funding and a $406 million cut to a fund to train and equip U.S. partner forces in Iraq and Syria for the fight against Islamic State.
Trump has threatened a government shutdown several times since taking office in 2017 in a bid to get his immigration priorities in congressional spending bills, especially funding for a wall along the southern U.S. border. Trump has asked for $25 billion to build the wall.
Congress must agree on a spending measure to fund the government by a Sept. 30 deadline, or the federal government will be forced to suspend all but the most essential operations.
(Reporting by Patricia Zengerle; Editing by Cynthia Osterman)