In April 1943 he commanded the LXXXII Army Corps, and from 25 June the 17th Army in the Caucasus and later the Crimean Peninsula. In a 29 April 1944 meeting with Adolf Hitler in Berchtesgaden, Jaenecke insisted that Sevastopol should be evacuated. He was relieved of his command afterward.
Later, he was held responsible for the loss of Crimea, arrested in Romania and court-martialed. Heinz Guderian was appointed as a special investigator in the case. Guderian proceeded slowly and eventually Jaenecke was quietly acquitted in June 1944. Jaenecke was dismissed from the army on 31 January 1945. On 15 June 1945 he was arrested by the Soviet authorities and sentenced to 25 years of hard labor for war crimes committed under his army command in 1942. He was released in 1955.
Scherzer, Veit (2007). Die Ritterkreuzträger 1939–1945 Die Inhaber des Ritterkreuzes des Eisernen Kreuzes 1939 von Heer, Luftwaffe, Kriegsmarine, Waffen-SS, Volkssturm sowie mit Deutschland verbündeter Streitkräfte nach den Unterlagen des Bundesarchives [The Knight's Cross Bearers 1939–1945 The Holders of the Knight's Cross of the Iron Cross 1939 by Army, Air Force, Navy, Waffen-SS, Volkssturm and Allied Forces with Germany According to the Documents of the Federal Archives] (in German). Jena, Germany: Scherzers Militaer-Verlag. ISBN978-3-938845-17-2.