The measure passed on a 336-75 vote.
The legislation would give the intelligence director exclusive authority over the estimated $40 billion intelligence budget, which was the top recommendation of the 9/11 Commission.
The legislation also creates a national counterterrorism center, an independent civil liberties board, increased security measures for airports, national standards for drivers licenses and other identification cards, increased mandatory sentencing for terrorist-related crimes, more border agents and inspectors, as well as increased detention spaces for terrorists.
"I think we have a significantly better bill than we did 17 days ago," said House Majority Whip Roy Blunt, R-Mo.
House leaders conducted a head count Tuesday afternoon to ensure the "broadest support possible" among Republicans, one House aide said. Rep. Mike Pence, R-Ind., said the meeting was "cordial, collegial, blunt but not hostile."
Sensenbrenner told the House Republican Conference he would oppose the bill, according to two GOP members. Sensenbrenner said Monday night the bill is "woefully" incomplete because it did not include certain immigration provisions.
The White House and GOP leaders have tried to pacify Sensenbrenner and other GOP members in his camp with assurances that the House would take up those items early next year. "We'll find must-pass legislation," Blunt said.
House Rules Committee Chairman David Dreier, R-Calif., whose panel crafted a "same-day" rule for the agreement Monday night, described the compromise as "the best we could do at this point."
House Intelligence Committee Chairman Peter Hoekstra, R-Mich., who chaired the House-Senate conference committee that produced a compromise bill, said there was a "tremendous amount of passion" for the immigration issues Sensenbrenner fought to include in the final bill.
The compromise measure dropped House provisions backed by Sensenbrenner that would have barred states from giving out drivers' licenses to illegal immigrants and set stricter criteria for asylum claims.
House Armed Services Committee Chairman Duncan Hunter, R-Calif., a key player in the negotiations, touted language added Sunday by conferees specifying that creation of a director of national intelligence would not interfere with the Pentagon's existing authority to direct the flow of intelligence needed by the armed services.
In the Senate, Republican leaders were debating whether to pass the bill by unanimous consent or roll call vote. It appeared likely the Senate would not consider the measure until Wednesday at the earliest.
Senate Governmental Affairs Committee Chairwoman Susan Collins, R-Maine -- who was extensively praised today by her colleagues for her efforts to finish the bill -- singled out the last-minute efforts by Sen. Trent Lott, R-Miss., to broker a deal.
"I kept calling Trent and he always gave me wonderful advice and intervened with some of his former colleagues in the House," Collins said.