The 56-year-old Sudanese doctor died in the early hours of Tuesday morning, after he was flown to Germany from Liberia on Thursday for treatment at St Georg Clinic in Leipzig.
On arrival from Liberia, doctors warned his condition was "highly critical, but stable".
The man was transported from Leipzig airport to the hospital last Thursday morning under tight security and treated on an isolation ward.
But the hospital said on Tuesday that "despite intensive medical measures and maximum efforts by the medical team, the 56-year-old UN employee succumbed."
He was the third Ebola patient from Africa to be treated in Germany since the outbreak started in West Africa this year.
One doctor from Uganda arrived in Frankfurt in early October and is currently undergoing treatment at the city's University Clinic. A patient from Senegal was treated in Hamburg and cured of the disease after five weeks in hospital.
Leipzig's St Georg Clinic can handle up to 12 cases of Ebola in six separate rooms. It is one of just seven hospitals in Germany with such a highly-rated isolation ward.
On Monday, Germany's health ministry suggested further Ebola cases could arrive from West Africa, announcing that they had 50 beds available for patients of the fatal disease.
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It is the first recorded case of anyone dying from Ebola in Germany.
The outbreak has claimed the lives of more than 4,000 people so far and infected around 8,400 people, according to the World Health Organisation (WHO).
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