Mr. Bush also signed 15 other bills, including the patch to the alternative minimum tax, reports CBS News White House correspondent Mark Knoller.
Mr. Bush's signature on the massive spending bill capped a long-running battle with the Democratic-run Congress as he left boarded Air Force One to fly from his Maryland mountaintop retreat and flew to his Texas ranch here to see in the new year.
Mr. Bush had deep reservations about special "earmark" spending in the bill, but signed it into law nevertheless.
"The omnibus (bill) funds the government at responsible levels that the president proposed without raising taxes," White House spokesman Scott Stanzel told reporters traveling to Texas with Bush.
Stanzel said that although he signed the bill, Mr. Bush continues to be "disappointed with Congress' addiction to earmarks."
"And soon the president will outline his fiscal year 2009 budget proposal," the spokesman added, "which will hold the line on spending, keep taxes low and continue us on the path to a balanced budget."
Mr. Bush, who had used his veto power to remain relevant in the debate with Democrats on national spending priorities, had agreed to sign the measure, which includes $70 billion for military operations in Iraq and Afghanistan, after winning concessions on Iraq and other budget items. The bill bankrolls 14 Cabinet departments and federal agencies and funds foreign aid for the budget year that began on Oct. 1.
Mr. Bush and his Senate GOP allies forced the Iraq money upon anti-war Democrats as the price for permitting the year-end budget deal to pass and be signed.
Democrats tried to use war spending legislation to force a change in Mr. Bush's Iraq policy, chiefly by setting a withdrawal goal with dates such as Dec. 15, 2009. But Mr. Bush and Republicans held a powerful hand. They knew Democrats would not let money lapse for troops overseas. That allowed a Bush veto in May and GOP stalling tactics to determine the outcome.
On the domestic budget, Mr. Bush's GOP allies were divided over whether the overall spending bill was a victory for their party in the long fight with Democrats over agency budgets.
Conservatives and outside watchdog groups criticized the bill for having about $28 billion in domestic spending that topped Bush's budget and was paid for by a combination of "emergency" spending, transfers from the defense budget and other maneuvers.