A consumer group had asked the Supreme Court for an emergency stay, which a federal appeals court refused earlier.
Justice Ruth Bader Ginsburg, who oversees the part of the country that includes New York, refused the stay request Saturday night.
CNN reported that Ginsburg's action clears the way for the two airlines to sign papers before the markets open Monday, though passengers will be booking flights through the individual airlines for the foreseeable future.
The group of passengers had complained the merger would result in high fares and reduced flights.
The combined company would be the largest airline in the world, CNN said.