The bill sailed through by a vote of 98-0 after senators added money to help track down Al Qaeda leader Usama bin Laden and fight the opium trade in Afghanistan that is helping fuel the Taliban's resurgence.
The overwhelming support for the overall bill and the money to support U.S. troops in harm's way came despite increasing criticism by Democrats of the Bush administration's handling of the war in Iraq.
The bill now totals $469.7 billion. It grew by more than $16 billion during a debate that began in July before it was suspended during lawmakers' four-week August recess.
By a 96-0 vote, senators approved $200 million to revive a CIA unit dedicated to hunting down bin Laden and other Al Qaeda leaders. News accounts in July said a CIA unit dedicated to capturing bin Laden had been disbanded.
"What does it say to violent jihadists that a terrorist mastermind remains alive and well five years after killing 3,000 Americans?" said Sen. Kent Conrad, D-N.D. "Our bill tells the terrorists that protecting our nation is the first priority — and that we are going to deliver to bin Laden the justice that a mass murderer deserves," said Conrad, who sponsored the legislation with Sen. Byron Dorgan, D-N.D.
Intelligence officials have said the realignment of CIA efforts on Al Qaeda reflects a view that the terrorist group is not as hierarchical as it used to be, as well as a concern about Al Qaeda-inspired groups that have begun carrying out attacks independent of bin Laden and his deputy, Ayman al-Zawahri.
Sen. Ted Stevens, R-Alaska, said the amendment was unnecessary because the overall defense measure has plenty of money to pursue Al Qaeda's leaders.
Senators also voted 51-45 in support of an amendment by Sen. Charles Schumer, D-N.Y., to provide $700 million for Pentagon efforts to combat the opium trade in Afghanistan.
The Defense Department bill originally contained $50 billion for military operations in Iraq and Afghanistan. Some $13 billion was added last month to pay to replace Army and Marine Corps equipment lost or worn out in harsh conditions in Iraq and Afghanistan.
Lawmakers expect an additional $7 billion will be added during House-Senate talks on a compromise bill. The comparable level of defense funding passed by the House in June was $458.6 billion.
With the latest infusion of war funds, Congress will have approved about $500 billion for the wars in Iraq and Afghanistan and other anti-terrorism efforts in the five years since the Sept. 11 terrorist assaults, according to the Congressional Research Service.
Appropriations for the Iraq and Afghanistan wars averaged almost $10 billion per month for the current year, so President Bush early next year will have to make another request for money for military operations in Iraq.
The bill also contains $1.8 billion to construct 370 miles of fencing and almost 500 miles of vehicle barriers along the U.S.-Mexico border.
The border security money would break budget caps set this year. But there is election-year urgency to take at least some steps on illegal immigration because GOP efforts to pass a broad immigration overhaul have stalled.
The Pentagon spending bill, a homeland security measure and perhaps legislation with money for veterans' programs will probably be the only annual appropriations bills to pass Congress by the Oct. 1 start of the new budget year.
The rest of the spending bills covering domestic agencies will wait until a lame-duck session after the Nov. 7 elections.
The defense bill contains $99 billion for personnel costs; $126 billion for operations and maintenance; $81 billion for weapons procurement; and $73 billion for research and development.
The Senate cut about $2 billion from Bush's targets for procurement of new weapons. That includes $250 million from the Army's request of more than $3.5 billion for the Future Combat System. It is the service's key weapons program and is expected to produce more than a dozen manned and unmanned vehicles and aircraft for combat.
To a considerable degree, the defense bill demonstrates the flexibility with which the Congress and the administration treat budget limits set on the Pentagon. But senators from western states also succeeded in adding $275 million at the last minute to combat wildfires.