The 34-year-old attacker "was critically injured in a shootout with police officers as he left the disco, and later succumbed to his wounds in hospital," police said in a statement.
Police said they did not believe that a nightclub shooting in the southern city of Constance was a terror attack.
"We're not assuming that this is an act of terrorist violence," Fritz Bezikofer told rolling news channel NTV.
Officers began receiving emergency calls from terrified clubbers at around 4:30 am (0230 GMT) after the man began shooting in the nightclub in an industrial zone in the city of Constance, killing one person on the spot and leaving three other people seriously wounded.
Shortly after he left the building, he was shot by police. One officer was also injured in the exchange of fire.
Police officers stand at the door of the night club 'Grey' in Konstanz, Germany, 30 July 2017 (AAP) Source: AAP
Terrified nightclubbers had either fled the building or found a place to hide, police said, adding that the danger was now over.
Helicopters were circling overhead and special forces were also deployed to secure the site.
Local broadcaster SWR reported witnesses saying that the gunman was armed with an automatic pistol.
A bouncer at the site had sought to stop the attacker, but was himself injured by the man, SWR said.
The shooting came just two days after Germany was shaken by a knife attack in the northern port city of Hamburg.
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A 26-year-old Palestinian had killed one and injured six in an assault at a supermarket.
He was a known Islamist with psychological problems, and investigators say his motives remain unclear.
Germany has been on high alert about the threat of a jihadist attack, especially since last December's truck rampage through a Berlin Christmas market that claimed 12 lives.
But it has also been hit by other assaults unrelated to the jihadist threat.
Among the deadliest in recent years is a Munich shopping mall rampage by 18-year-old German-Iranian man which left 10 people dead including the gunman himself.
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