The two cubs were born in mid-January to Misha and Masha, brown bears donated to the Dählhölzli zoo in 2009 by then Russian president Dmitry Medvedev and his wife as a gift to the Swiss capital.
Last week, critics slammed the zoo for not separating the bears after Misha, a 360-kilogram adult, killed one of the two cubs, known as “Baby Bear 3”.
The zoo maintained it wanted to give the animals the most natural environment possible and it feared that separating the adults would be disastrous, leading to “massive behavioural disorders”.
But it said on Monday it was forced to subject “Baby Bear 4” to euthanasia to prevent “further distress and pain” to the cub, which was being batted around by the father bear.
Animal rights groups said the zoo took the wrong approach and the deaths of the two cubs could have been avoided.
“We strongly condemn the incidents that have led to the unnecessary and painful death to bred bear cubs,” the Swiss Animal Protection group said in a statement.
Last week, the zoo’s management said it was not planning to separate the parent bears to protect the remaining cub.
While acknowledging the risk to the offspring, it said it wanted to keep the bears in as "natural" an environment as possible.
But animals rights activists say the environment in the zoo is not natural for the bears, pointing out that there was not enough space for the male bear to be properly separated.