A company spokesman said short and medium haul flights were back to normal on Sunday, but a small number of long-haul flights had still been cancelled.
Originally, the pilots' union Vereinigung Cockpit had initially called for a 24-hour walkout on Wednesday, but subsequently extended the industrial action over four days.
The stoppages had targeted short and medium haul services on Wednesday and Friday and long haul and cargo flights on Thursday and Saturday.
In all, around 220,000 passengers have been hit by the four days of walkouts, Lufthansa calculated.
It is the 12th and longest stoppage since the pilots began their industrial action last April.
The dispute hinges on plans by Lufthansa to scrap an arrangement under which pilots can retire at 55 and receive up to 60 percent of their pay until they reach the statutory retirement age of 65.
Pilots are also concerned about Lufthansa's aim to further develop its low-cost activities as it faces growing competition.