Pilot union Vereinigung Cockpit called on pilots at Eurowings, Germanwings and Lufthansa CityLine to walk off the job for two and a half hours to apply pressure in wage talks, spokesman Markus Kirschneck told German news agency DDP/Dow Jones on Wednesday.
About 200 pilots and co-pilots participated in the strike until 8 a.m., delaying about 100 flights.
Among the airports affected were Frankfurt am Main, München, Düsseldorf, Köln, Berlin Tegel and Schönefeld, Hamburg, Nürnberg, Stuttgart, Bremen, Paderborn, Münster-Osnabrück, Friedrichshafen and Dresden.
Cockpit is negotiating with Deutsche Lufthansa AG over contracts for pilots at all three smaller airlines affected by Wednesday's strike. The contracts are independent of one another.
The union has said negotiations that have lasted for months are at a standstill, announcing most recently on Tuesday that talks over Lufthansa CityLine had broken down.