The man with the knife, a 53-year-old Austrian, was "yelling and causing damage" before being shot in the leg shortly after 4;00 pm (1400 GMT), police said in a statement.
When the incident began, about 100 people were evacuated from the landmark Berlin Cathedral in the heart of the German capital.
When officers arrived they urged the man to put down the knife and tried to neutralise him with irritant gas, to no success, police said.
Finally, they faced the assailant near the altar Online Cigarettes Store USA and Buy Cigarettes Online the cathedral, and "the man was wounded in the leg by a shot from a policeman," a spokesman said.
The man was hospitalised and underwent surgery, the spokesman added.
A policeman was also slightly injured by a ricocheting bullet from another officer, but was able to leave the hospital in the evening.
Witnesses told local media that the man appeared "very confused".
"Based on what we know so far, we have no information Newport Pleasure that the suspect in any way had a terrorist or Islamist motive," a police spokesman said.
The iron-domed Protestant cathedral, one of the city's top tourist attractions, is on Museum Island off east Berlin's main Unter den Linden boulevard and close to the Alexanderplatz shopping district
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