Mullah Abdul Rahman was described as a "shadow governor" in Kunduz province.
According to the Bild report on Tuesday Germany's elite force, the 'Kommando Spezialkräfte', or KSK, was involved in an operation late last week that led to the capture of the Taliban leader.
Bild quoted a Bundeswehr spokesperson as saying that the "operation led by Afghan special forces was conducted in association with ISAF forces - among them German forces" on Friday.
Mullah Abdul Rahman was reportedly apprehended alongside one other person as he attended a meeting of senior Taliban leaders in the village of Ghundaj Kalai in the northern Kunduz province.
He had been blamed for an attack on the Bundeswehr on Good Friday, 2010, which resulted in the death of three German soldiers.
NATO has more than 100,000 troops, including the German deployment, in Afghanistan fighting the Taliban insurgency. A NATO pull-out is scheduled by the end of 2014 with newly trained Afghan forces due to take over security.
ccp/rg (AFP, dpa)