Sanders is calling on President Obama to announce a new executive action.
House Democratic leaders had urged members to oppose the spending bill.
Obama has threatened to veto the circumvention of spending caps.
Congress faces a May 31 deadline to keep federal transportation funding flowing.
The House is expected to pass a $612 billion policy bill despite Democratic opposition.
The proposal would aim to close the facility by the end of 2017.
Cristina Marcos 05/14/15 07:09 PM EDT
The House voted to strip the provision from the annual defense bill.
The vote is a victory for members who pushed for an oversight role in the nuclear talks.
Two days after rejecting it, the Senate agrees to take up fast-track.
Kristina Wong 05/14/15 01:41 PM EDT
Coffman urges opposition to amendment set for vote on Thursday.