The measure passed 96-0 as an amendment to a comprehensive financial regulation bill before the Senate.
The U.S. central bank also would have to post on its Web site information regarding those loans, including the identity of the recipients.
The one-time audit would be carried out by Congress' investigative arm, the Government Accountability Office, and cover a period beginning in December 2007. At its peak, at the end of 2008, the Fed's lending totaled $1.16 trillion.
The proposal gained momentum after its lead sponsor, Sen. Bernard Sanders, an independent, narrowed the audit's scope and the Obama administration dropped its objections.