The bear, a two-year-old identified as M13, was shot in the Poschiavo area, where it had awoken from its hibernation and come into contact with a 14-year-girl and a pair of Italian tourists.
The girl was taken to hospital and treated for shock after the burly bruin followed her through part of the town near the Italian border.
Wildlife officials determined the bear was a security risk, although the decision was condemned by many environmentalists.
Provisions of Switzerland's bear management plan allow for bears to be destroyed in such cases.
The killing of M13 marks the first time since 2008 that Swiss officials have shot a bear.
In that year, a bear identified as JJ3 was killed after also being judged a nuisance.
M13 had caused problems in the Poschiavo area since the spring of 2012 when it was anesthetized and tagged with a tracking transmitter after preying on a goat.
The bear ended up being injured by a train before being caught dining on sheep in September.
In October, officials were forced to erect an electric fence around a school in Poschiavo after the bear was was discovered eating honey at an aviary outside the building.
Then in November, he broke into a shed next to chalet, where he spent 36 hours.
The bear ate potatoes stored in the hut, as well as stale bread, and destroyed equipment in the building before moving on.
The dramatic encounter with a 14-year-old girl, identified as Emina Piana, on Saturday brought things to a head.
The Poschiavo council demanded action from authorities, who responded.
Culling of bears is a sensitive subject in Switzerland.
Joanna Schoenenberger, bear specialist with environmental group WWF Switzerland, maintained it was not necessary to kill M13.
"There were other solutions than to kill it," she told Le Matin.
"As well, it was not aggressive and posed clearly fewer problems than JJ3, who was killed in 2008 after a lot longer period of observation."
M13 was one of just a handful of bears left in the country, and the only one being tracked in Switzerland.
The animals were hunted to extinction but began to reappear in 2005 after being reintroduced in a Trentino nature park in Italy, not far from the Swiss border.
Since then, a few bears have wandered back and forth across the border.