Some 45 to 46 flights between 5:30 am and 8 am were cancelled.
Shortly before the end of the walkout at 8 am, a Lufthansa spokesperson said at least 28 flights had been cancelled, telling news agency DDP that some 1,200 passengers had been affected.
The pilot union Cockpit called the strike at the last minute, affecting airports in Munich, Düsseldorf and Stuttgart most severely. Airports in Berlin, Hamburg, Bremen. Cologne, Nuremberg, and Dresden, were also hit.
Flights remained on the ground after the strike's end, but airports said they planned to return to schedule as soon as possible.
The pilots are demanding salary increases. On May 21 pilots from CityLine, Germanwings, and Eurowings staged another limited strike.
The Cockpit union is demanding the pay raise for some 1,500 pilots, but has not given concrete figures.
On Monday the union called for pilots to vote on whether to stage indefinite strikes.