"It is with relief that we are able to return to scheduled service on the routes to Tel Aviv," the company said in a statement
On Thursday, US airlines lifted their bans on flights to Tel Aviv's Ben Gurion International Airport, which were imposed on Tuesday after a rocket fell close by. The European air safety agency has also lifted its warning on flights to the Jewish state.
But on Friday an Air Canada flight from Toronto was forced to circle the airport before landing after rockets were fired, an airline spokeswoman said.
Lufthansa currently operates up to ten daily flights to Tel Aviv from Berlin, Frankfurt, Munich, Vienna and Zurich.
Passengers affected by the suspension could choose to either be reimbursed or could exchange their tickets, it said.