Doctors at the hospital in Leipzig said the man, 56, originally from Sudan, died despite receiving experimental drugs to treat the virus.
More than 4,400 people have died from the outbreak, mainly in West Africa.
The rate of new cases at some of the "epicentre" areas has slowed down, the World Health Organization says, but the number of cases in the capitals of the worst-affected countries is rising.
Senior WHO official Bruce Aylward told reporters on Monday that the outbreak was also continuing to spread geographically to new districts in the capitals of Sierra Leone, Liberia and Guinea.
Elsewhere:
*In all cases but two, first in Madrid and later in Dallas, the patient was infected with Ebola while in West Africa.
How not to catch Ebola:
Why Ebola is so dangerous
How Ebola attacks
Ebola: Mapping the outbreak
The man who died in Leipzig had been working as a UN medical official in Liberia - one of the worst affected countries - when he caught Ebola.
He arrived in Germany last Thursday 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 BBC's Jenny Hill in Berlin says.
He was also the third Ebola patient to be treated for the virus in Germany after contracting the disease 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 World Health Organization (WHO) says it is alarmed by the number of health workers exposed to the disease.
The WHO has warned the epidemic threatens the "very survival" of societies and could lead to failed states.
Source: WHO
Note: figures have occasionally been revised down as suspected or probable cases are found to be unrelated to Ebola. They do not include one death in the US recorded on 8 October.

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27 August 2015 Last updated at 17:56 BST
Both games are free to play but have some features which cost money to add.
The Advertising Standards Agency, the UK authority in charge of checking advertising, say that the games put too much pressure on children to buy these additional features.
That's because they say things like 'Moshi Monster needs you', or tells players they will be 'super popular' if they pay to become members.
Now the companies behind both Moshi and Bin Weevils say they have changed the games and will stick to the rules in the future.
Watch Newsround reporter Jenny's full report on this.
A UN medical worker infected with Ebola has died at a hospital in Germany.
[NEXT_CONCEPT]
The popular online games Moshi Monsters and Bin Weevils have found themselves in trouble for putting unfair pressure on children to make in-game purchases.