Air traffic controllers voted earlier this week by a huge majority to strike for six hours on Thursday to push for a pay increase and better working conditions.
But Deutsche Flugsicherung (DFS), the company responsible for air traffic, disputed the strike's legality and applied for a temporary court injunction against it.
The labour court in Frankfurt ruled some of the demands of air traffic controllers' union GdF were invalid and therefore a strike was not a legal way to press their case.
The strike could have affected up to 2,500 flights between 6 am and noon on Thursday, hitting travellers at the height of the holiday season.
Out of a total of 5,500 air controllers in Germany, 3,400 belong to the GdF union, which had called for all its members to walk off the job.
In a statement, DFS said it was willing to negotiate with the union and said the strike would “be at the expense of travellers and holidaymakers.”
Over 95 percent of union members voted for all-out strike action on Monday.
The union is demanding a 6.5 percent pay increase for its members, along with better working conditions, but management has offered just 4.1 percent over two years, according to a union statement. At the moment, controllers start at €90,000 ($128,000) per year.