Democrats now face difficult choices and weeks of work on the leftover budget, which totals $463 billion and must be passed at Bush's strict budget limits.
"They are leaving us with a tremendous mess," Senate Minority Leader Harry Reid told reporters. "We have alternatives, none of which are very good."
Democrats made good on a promise to block an automatic congressional pay raise until the minimum wage is increased.
The House of Representatives also approved, 330-59, an agreement to allow U.S. shipments of civilian nuclear fuel to India, an administration priority that is opposed by some because India, which has nuclear weapons, has not submitted to full international inspections. The Senate quickly cleared the bill for Bush's signature.
The trade measure establishes permanent, which is generally supported, with the extension of trade benefits for sub-Saharan Africa, Haiti and Andean nations. The Haiti provisions in particular raised red flags with lawmakers trying to protect home-state textile industries.
Eight Republican senators from North and South Carolina, Georgia, Alabama and Kentucky on Thursday wrote to congressional leaders saying 100,000 textile jobs in their region had already been lost due to trade agreements and they would oppose "as forcefully as possible" the Haiti measure. But of the eight, only two followed through on threats to oppose the Haiti trade preference after it was added to the broader bill.