The strike ended on time despite a spokesman for the pilots' union raising the possibility of the action continuing into the weekend.
Aircraft out of position and delays could mean that the airline will cancel further flights in the afternoon.
Vereinigung Cockpit (VC) began the industrial action at 6am on Friday at all airports in the country used by Germanwings. It was due to last until midday.
The spokesman described the present action as "pinpricks" aimed at bringing management back to the negotiating table.
The worst-affected airports are Cologne and Stuttgart, but Düsseldorf, Berlin, Hanover, Hamburg and Dortmund have all seen flights cancelled.
At the Cologne/Bonn airport 32 of 50 scheduled flights were struck off departure boards, while at Stuttgart 22 of 36 were cancelled.
Lufthansa wants to raise the retirement age for its pilots from 59 to 65, while the union wants Lufthansa to keep paying transition money to those who retire before 65.
The disagreement led to a three-day strike in April which grounded 3,800 flights and affected 425,000 passengers.
After the April strike, negotiations started again but broke down last Friday.