The remains of the two German soldiers arrived at an air force base near the western German city of Cologne on Saturday night. Family members and fellow soldiers were present.
German Defense Minister Ursula von der Leyen also attended the private ceremony before leaving for Mali and Niger later in the evening.
Von der Leyen said earlier that she wanted to spend more time with German troops stationed in West Africa as part of the UN peacekeeping mission there. She will also meet her counterpart in Niger and speak to the country's president as well.
During her visit, the minister is expected to meet with her French counterpart, who wants Germany to take on a larger role in peacekeeping missions across former French colonies in Western Africa.
The two soldiers killed in the crash came from the central German state of Hesse and were stationed at a base in the town of Fritzlar. Their Tiger attack helicopter crashed on Wednesday near the town of Tabankort in the Gao region of Mali.
The two pilots were conducting a surveillance flight for the UN peacekeeping mission in Mali (MINUSMA) in the aftermath of violent clashes between armed groups.
The deaths were the first losses for Bundeswehr troops in Mali, and the first death of a soldier on deployed mission in nearly two years.
The cause of the crash remains unknown, although there was no evidence to suggest that the helicopter was deliberately shot down.
A German Defense Ministry spokesperson reported that aviation experts in Mali had found one of the helicopters two flight recorders on Saturday, but in a considerably damaged state. It is not yet clear whether information can be extracted from it. The second flight recorder has not yet been found.
A total of 875 German soldiers are stationed in Gao as part of the UN's Mali peacekeeping operations.
ss/jm (dpa, Reuters)