"Air traffic facilities will begin to return to regular staffing levels over the next 24 hours," the FAA said in a statement.
The U.S. House Friday passed a bill aimed at ending sequester-related flight delays by restoring funding for air traffic controllers.
The Senate approved the same bill Thursday evening by unanimous consent.
The furloughs, which started Sunday, required a day off without pay for every 10 workdays, or a total of 11 days off, through the end of the fiscal year ending Sept. 30.
The result was about 10 percent of the 15,000 air-traffic controllers were off every day.
The furloughs were prompted by $85 billion in across-the-board federal spending cuts, known as the sequester, that were required under a 2011 deal to raise the federal borrowing limit.