The measure gives the secretary of transportation the flexibility to transfer funds earmarked for capital improvements to prevent reduced operations and staffing of the Federal Aviation Administration as a result of the sequester, which required across-the-board spending cuts.
Lawmakers feared the furloughs would create unacceptable flight delays at the nation's airports and rushed legislation through Congress last week.
The furloughs began April 21 but with passage of the measure, the FAA suspended them Saturday night.
The furloughs required a day off without pay for every 10 workdays, or 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.