The airline's application for a court injunction against the walkout -- the 13th in 18 months -- was turned down by Frankfurt's labour court late yesterday.
The strike, which was called by pilots' union Vereinigung Cockpit, initially affected long-haul flights yesterday, but the union later expanded it to include short- and medium-haul services today to turn up heat on the management.
Management and the unions have been locked in a bitter dispute since April 2014 over plans to change the pilots' early retirement arrangements.
Out of a total 1,520 Lufthansa flights that should have flown on Wednesday, only around 500 would go ahead, the carrier said.
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The strike only affects Lufthansa services, while flights by its subsidiaries - Germanwings, Swiss, Austrian Airlines and Brussels Airlines - would operate normally.
Passengers on domestic flights are being allowed to swap their tickets for a ticket on the German national railway, Deutsche Bahn.
In the past 18 months, pilots have staged repeated walkouts, but suspended industrial action in March after a Germanwings jet crashed in the French Alps in an incident blamed on a suicidal co-pilot.
The dispute hinges on plans by Lufthansa to scrap an arrangement under which pilots can retire at 55 and receive up to 60 per cent of their pay until they reach the statutory retirement age of 65.