The authorities said the youngster, who fell 10 to 12 feet at Cincinnati Zoo, is expected to recover after being picked up out of the moat and dragged by the gorilla for about 10 minutes.
He was taken to Cincinnati Children’s Hospital Medical Centre, and zoo officials said he was alert when he was transported there.
Director Thane Maynard said the zoo’s dangerous animal response team decided the boy was in “a life -threatening situation” and that they needed to put down the 400lb-plus male gorilla, who was named Harambe and was aged 17.
“They made a tough choice and they made the right choice because they saved that little boy’s life,” he said.
“It could have been very bad.”
He said he had not yet talked to the boy’s parents.
The authorities are still investigating, but zoo officials believe that the boy crawled through a railing barrier, then fell into the moat.
Mr Maynard said the gorilla did not appear to be attacking the child, but that it was “an extremely strong” animal in an agitated situation.
He said tranquillising the gorilla would not have knocked it out immediately, leaving the boy in danger.
Mr Maynard said it was the first time that the team had killed a zoo animal in such an emergency situation, and he called it “a very sad day” at the zoo.
The lowland gorilla is an endangered species.
The incident was reported at around 4pm local time on Saturday, and the area around the gorilla exhibit was closed off after zoo visitors reported hearing screaming.
Harambe had come to Cincinnati Zoo only last year from the Gladys Porter Zoo in Brownsville, Texas.
Mr Maynard said that Cincinnati’s Gorilla World area would be open as usual yesterday, and zoo officials believe the exhibit remains safe.
The zoo prides itself on its work in protecting endangered species, and has been part of successful captive breeding efforts in recent years in the effort to save the endangered Sumatran rhino.