The three German soldiers were killed earlier on Friday while battling Taliban fighters in the restive northern province.
The Germans had been on a bridge-building and mine-clearing mission when they were ambushed by Taliban fighters who had laid bombs along the roadside.
A correspondent for the German weekly magazine Der Spiegel said that around 200 Taliban fighters had staged the ambush, adding that he had seen a vehicle blown up by a mine.
Fighting continued into the evening, and the Afghan army were deployed to offer assistance to the German troops. As they approached in the dark, the Germans opened fire on their vehicle.
German troops control much of northern Afghanistan, which is relatively peaceful.
But security in the area the attacks took place is volatile, and last month a German general said that the Nato force in Afghanistan was planning an offensive against the Taliban in the area later this year.
Bruno Kasdorf, the chief of staff at the International Security Assistance Force (Isaf), refused to give further details of the planned offensive, but said it would be on a "similar" scale to the ongoing operation in Helmand province, where 15,000 troops have been deployed.
Thirty-nine German troops have now been killed in Afghanistan since troops arrived in 2002.
The German contingent in Isaf is currently 4000-strong, and 850 extra troops are set to be sent to Afghanistan after German politicians voted in favour of extending the mission there by another year.
Twenty-two German soldiers have been killed by fighting or attacks in Afghanistan since 2001 and another 138 wounded, according to the German defense ministry.