The 56-year-old man, originally from Sudan, died despite receiving experimental drugs to treat the virus, German doctors say.
The Ebola outbreak has killed more than 4,000 people since March – mostly in Liberia, Sierra Leone, Guinea and Nigeria.
The World Health Organization (WHO) says the outbreak is the “the most severe, acute health emergency in modern times”.
The man had been working as a UN medical official in Liberia – one of the worst affected countries – when he caught Ebola.
He arrived in Germany on October 9 for treatment and was put into a hermetically sealed ward, accessed through airlock systems.
“Despite intensive medical measures and maximum efforts by the medical team, the 56-year-old UN employee succumbed to the serious infectious disease,” a statement from St Georg hospital said.
He was the second member of the UN team in Liberia to die from the virus.
The man was the third Ebola patient to be treated for the deadly virus in Germany after contracting the disease in the outbreak zone in West Africa.
One patient – a Ugandan doctor infected in Sierra Leone – is still receiving treatment in a hospital in Frankfurt, while a Senegalese aid worker was released from a hospital in Hamburg after five weeks of treatment.
The WHO says it is alarmed by the number of health workers who have been exposed to the disease.
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