The three-year-old boy clambered through a barrier and then fell 10 feet into a moat. He was then grabbed and dragged by the 400lb (180kg) gorilla. Zoo officials say they decided to shoot the animal as it was a "life-threatening" situation.
A Cincinnati fire department incident report stated that the gorilla "was violently dragging and throwing the child" when they were called to the scene, according to Cincinatti's WLWT.
The officials "made a tough choice and they made the right choice because they saved that little boy's life. It could have been very bad", zoo director Thane Maynard said in a BBC report.
He added that although the toddler's life was not being attacked by the gorilla, he "certainly was at risk". Cincinnati zoo temporarily closed its gorilla zone following the incident on Saturday 28 May.
"We are all devastated that this tragic accident resulted in the death of a critically endangered gorilla. This is a huge loss for the zoo family and the gorilla population worldwide," Maynard said.
The zoo's dangerous animal response team killed the gorilla about 10 minutes after the boy fell into the enclosure. The boy was in between the gorilla's legs when the gorilla was shot, according to fire officials. The decision to shoot the animal was taken because a tranquiliser would not have acted fast enough, Maynard added.
Video footage shows the three-year-old being dragged across the moat by the gorilla. The child was reportedly tugged around by the animal for 10 minutes. One woman said that she saw the gorilla pull the boy from one end of the enclosure to the other.
Another eyewitness said the child was conscious throughout his ordeal and rescue. After the boy was saved, he was taken to Cincinatti Children's Hospital where it is believed he will recover.
The 17-year-old gorilla called Harambe was born in captivity and transferred to Cincinatti zoo in 2014. Two female gorillas were present in the enclosure at the time of the incident and did approach the child.