Some 20-30 German troops have remained at Konya under an Airborne Warning and Control System (AWACs) mission, part of the US-led coalition's campaign against the Islamic State group in neighbouring Syria and Iraq.
The delegation had initially been due to come to Turkey in July for the routine visit, but the trip was blocked by Ankara.
Nato secretary-general Jens Stoltenberg then intervened and the visit was organised by the alliance, rather than Germany.
"We were received by high-ranking officials and the Turkish side was visibly eager to reduce tensions," Social Democrat (SPD) MP Rainer Arnold told AFP before boarding the plane to return to Berlin.
"The visit was a step in the right direction," he added.
Relations between Berlin and Ankara have deteriorated since last year's failed coup aimed at overthrowing President Recep Tayyip Erdogan, and a massive subsequent crackdown.
The deputy secretary-general of Nato, Rose Gottemoeller, led the delegation which included seven German MPs from different parties, according to the Bundestag.
"We expressly welcome the fact that this visit could take place," German foreign ministry spokesman Martin Schaefer said earlier Friday.
"A visit is a visit. It is already good... We will see how things continue," he said, adding that these types of visits organised within the Nato framework could not constitute "a lasting and sustainable political solution".
The row over MPs' access to German troops on Turkish soil boiled over in June when Berlin pulled out 260 troops from Incirlik base in southern Turkey and relocated them to Jordan, after Ankara repeatedly thwarted lawmakers' efforts to visit.
Germany has condemned the arrest of over 50,000 people, including German citizens, under the state of emergency imposed following the attempted putsch.
Ankara in response has repeatedly accused Berlin of supporting "terrorists", referring to Kurdish separatists and suspected coup-plotters.
Ties worsened this week after German Chancellor Angela Merkel announced her intention to seek an end to European Union membership talks with Turkey, which Ankara reacted to in anger, accusing German politicians of "populism".
Alexander Neu, an MP from the far-left Die Linke party, said Friday's visit did not address the Turkish-German tensions but only IS and the "exchange of information" on this subject, according to German news agency DPA.