Just over half of the carrier's scheduled 1,400 domestic and European flights taking off or landing in Frankfurt or Munich were cancelled, affecting around 80,000 passengers, a Lufthansa spokesman said.
Flights operated by Lufthansa's subsidiaries Germanwings, Eurowings, Swiss and Austrian Airlines were not affected, AFP reported.
But the pilots' union Cockpit announced that the stoppage would be extended to Thursday, when long-haul and cargo services would be hit.
It is the 12th walkout since last April over management plans to change the pilots' transitional pension arrangements.
Currently, pilots can retire at 55 and receive up to 60 percent of their pay until they reach the statutory retirement age of 65.
Lufthansa wants to scrap the arrangement.
In 2014, the repeated strikes cost Lufthansa an estimated 232 million euros ($245 million).