In an highly unusual meeting, Ambassador Martin Erdmann visited Turkish-German national Yucel at the high-security prison complex in Silivri near Istanbul, the German embassy said.
Imprisoned in February, Yucel has been personally accused by Turkish President Recep Tayyip Erdogan of working as a German agent.
The German embassy said in a statement that Erdmann met Yucel for over an hour. While consular officials regularly meet detained foreign nationals in jail, it is rare for the visit to be made by the ambassador.
"He is doing well. The support from Germany - the readings, concerts, car rallies, is helping him. He knows that he is not alone and won't be forgotten," the embassy said.
German Foreign Minister Sigmar Gabriel welcomed the visit but said "this does not change the fact... we demand a fair process and want to see him freed. We will continue working on this."
Chancellor Angela Merkel has closely followed Yucel's case, and brought up the issue on a number of occasions with Turkish authorities.
She has assured that Germany would do "everything in its power" to ensure Yucel's release.
The ambassador's visit came amid high tensions in bilateral ties between the two NATO allies.
Germany has voted to pull out its troops from Incirlik base in southern Turkey, used for raids against the Isis terror group in Syria, after Ankara blocked a visit by German lawmakers.
Turkey ranks 155 on the latest Reporters Sans Frontieres (Reporters Without Borders) world press freedom index, below Belarus and the Democratic Republic of Congo, after dropping four places from its 2016 ranking.
According to the P24 press freedom website, there are 167 journalists behind bars in Turkey, most of whom were detained as part of the state of emergency imposed after last year's coup attempt.
Turkey last week released and deported French photojournalist Mathias Depardon who was held for a month on charges of supporting terror groups in a case that amplified concerns over press freedom.