The new department will have about 170,000 employees and an annual $38 billion budget.
“It is landmark in its scope and it ends a session which has seen two years worth of legislative work which has been very productive for the American people,” the president told Republican lawmakers, according to the Associated Press.
Democratic attempts to pass an amendment that would have removed several contentious provisions from the bill were defeated 52 to 47.
Before the House passed a compromise version of the legislation last week, some members added provisions that would shield vaccine makers from potential lawsuits over negative effects the drugs may have on patients. Similar lawsuit protection was given to manufacturers of airport security equipment.
Other additions would allow companies that operate overseas — and don’t pay U.S. taxes — to still be awarded government contracts, and would create a homeland security research center at Texas A & M University.
Democrats said the new provisions amounted to special favors for Republican supporters. Some Republicans, like Sen. Phil Gramm of Texas, argued that companies producing products for a war effort have long been given legal protection.
Several GOP moderates balked at the new provisions and made Senate Minority Leader Trent Lott promise to reconsider them when the new Congress convenes in January.
Sen. Robert Byrd (D-W.Va.) said the Democratic amendment to remove the provisions was “the Senate’s last chance to show the American people that we are serious about placing some controls on this massive new bureaucracy.”
The Democratic effort was strengthened by the support of Republican Sen. John McCain of Arizona, while three Democrats, Sens. Mary Landrieu of Louisiana, Ben Nelson of Nebraska and Zell Miller of Georgia sided with Republicans. Independent Dean Barkley, an interim senator from Minnesota, also backed the GOP.
President Bush personally asked some lawmakers for help in defeating the Democratic amendment.
The House passed an earlier version of the bill in July, but it stalled in the Senate when Democratic lawmakers voiced concerns that it stripped federal workers of civil-service protection.
After Republican election victories on Nov. 5, a handful of Senate Democrats approved a version of the bill that gave the president the broad authority he sought over employees, but stipulated he must notify Congress and employee unions before waiving traditional worker rights in the name of national security.
Now the bill will be sent to the White House for the president’s signature.