The vote, on a provision attached to a student aid bill, was 345-75, with Democrats supplying all the "no" votes.
On Monday the Senate voted 83-7 to deny housing and community grant funding to ACORN, which stands for the Association of Community Organizations for Reform Now.
Republicans accelerated their attacks on the liberal-leaning group a year ago when ACORN, in conducting a massive voter registration drive, was accused of submitting some false registration forms.
On a hidden-camera video released on Monday, two ACORN employees are seen apparently advising a couple that was posing as a prostitute and her pimp to lie about her profession and launder her earnings. The video was the latest in a series that has already led to the firing of four ACORN employees in Baltimore and Washington. It was created by James O'Keefe and Hannah Giles and posted on BigGovernment.com, where O'Keefe identifies himself as an activist filmmaker.
ACORN spokesman Scott Levenson blasted the video shot at the organization's Brooklyn office, saying the group believes the voices of the couple were dubbed over to alter the conversation and make the interaction appear more objectionable than it may have been.
ACORN said Wednesday that it is ordering its own independent investigation of the incidents, while stressing that they were isolated cases.
The Census Bureau, meanwhile, also has severed its ties with the group for the 2010 national census.
Republicans have urged federal officials to go further by launching a comprehensive investigation of how ACORN spends and manages federal money.
"As long as taxpayers are subsidizing ACORN and its affiliates, we need to use every measure possible to ensure that those dollars are being spent and managed appropriately," said Rep. Darrell Issa, R-Calif., sponsor of the measure that passed the House.
The Senate and House initiatives to cut funding for ACORN won't take effect until the bills to which they are attached clear Congress and are signed by President Barack Obama. The Senate measure is attached to a fiscal 2010 spending bill.
"President Obama needs to indicate whether he'll sign this bill and join us in ending all taxpayer funds for this corrupt organization," House Republican leader John Boehner of Ohio said after the vote.
White House press secretary Robert Gibbs on Wednesday said the conduct seen on the tapes "is completely unacceptable." He said the Obama administration "takes accountability extremely seriously" and noted that the Census Bureau had determined that ACORN could not meet its goal for conducting a fair and accurate count next year.
House Speaker Nancy Pelosi, in a conference call with reporters, called the latest allegations against ACORN "horrible." However, she pointed out that ACORN has many honest employees and was conducting an internal investigation, and that it was up to House-Senate negotiators to determine whether the provision to cut funding would be in the final version of the bill.