Lufthansa said passengers would be able to show the digital proof of vaccination either on their phones or on a printout when checking in at the airport, and the boarding pass would then be issued.
"This eliminates the need to juggle different papers and proofs. It also significantly reduces the risk of misuse of fake vaccination certificates," Lufthansa said.
Germany started issuing QR codes for those who are fully vaccinated last week.
Germans are booking holidays again at rates higher than in 2019 before the coronavirus hit, TUI Group, the world's biggest holiday group, said on Wednesday.
Lufthansa said on selected routes it would also soon be possible to use the digital vaccination certificate to check in via smartphone using the airline's app.
Passengers who want to check they have the right paperwork can also contact the Lufthansa service centre up to 72 hours before they fly, which can also deal with proof of a negative COVID-19 test, recovery from the virus and also vaccinations.
Lufthansa said it still recommends that passengers carry their original printed vaccination certificates with them on their journey until further notice.
Lufthansa said earlier on Thursday its new subsidary focused on holiday flights, Eurowings Discover, will ramp up operations faster than expected this year, starting with a flight at the end of July from Frankfurt to Mombasa.
European Union countries agreed last week to an easing of travel restrictions over the summer that will allow fully vaccinated tourists to avoid tests or quarantines and broaden the list of EU regions from which it is safe to travel.
Britain is considering easing travel restrictions for double vaccinated people, a move which would placate airlines who are threatening legal action against the government's strict curbs on trips abroad.
(Reporting by Emma Thomasson; Editing by Gareth Jones)