The Land and Environment court overturned a previous ruling that would have banned airplanes, starting in 2018, from taking the straightest path to land on the one of the runways at the capital's main airport.
The earlier decision stated that planes would have to take a detour around the town Upplands Väsby and that only at extremely busy times would airliners be allowed to fly over the town.
Although the flight ban was thrown out, the court did tack on a condition requiring Arlanda to avoid directing planes over densely-inhabited areas when possible.
Business leaders welcomed the decision. Maria Ranka, president of the Stockholm Chamber of Commerce, greeted the news with a "sign of relief."
The decision can be appealed by 19 December 2014.