Lufthansa welcomed the ruling by the state labor court in Frankfurt but said that a special, reduced timetable it had drawn up for the day would remain in place.
It said that largely normal services would be resumed on Thursday.
The pilots' union, Vereinigung Cockpit, has been calling regular short-term strikes in the long-running labor dispute, which comes as Lufthansa restructures to meet increasing competition from Gulf airlines.
The pilots want the airline to keep making transition payments for those seeking early retirement.
Vereinigung Cockpit began its strike on long-haul flights Tuesday, forcing the cancellation of 90 flights, and extended the walk-out to medium-and short-haul flights today.
Union spokesman Markus Wahl told n-tv television after the ruling that it had told pilots to be available for work immediately. Today's ruling overturned one by a lower court yesterday that went in the union's favour.
Lufthansa said some 140,000 travelers were affected but that about 500 of the airline's flights were still in operation. Subsidiaries Germanwings, Swiss, Austrian Airlines or Brussels Airlines weren't involved.
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