The TV personality praised Harambe, a "glorious" critically-endangered 17-year-old primate, and castigated zoo-keepers' "failure" to make barriers secure for leading to his death.
Cincinnati Zoo had insisted they shot the 400lb animal when the situation became “life-threatening” for the child, who managed to climb through a public barrier and fell into the exhibit’s moat.
Harambe was filmed during the ordeal picking the child up and staying with him for about 10 minutes.
But critics of the zoo's decision to kill the gorilla came piling in, and were led by Morgan.
"RIP Harambe. A magnificent gorilla dies because a zoo failed to make its barriers safe," he wrote in a post on Twitter.
Many others piled in to lay blame at the zoo for its decision to shoot Harambe.
But one sympathetic commentator called for calm and said the zoo-keepers had been put in "the worst position possible" by being forced to make the decision, adding that they would have been devastated at having "lost a family member".
A petition was launched in the wake of the incident, urging police and zoo authorities to hold the parents of the child responsible for the “senseless death”.
A petition was launched around 5pm on Sunday and within an hour had almost 2,000 signatures.
It has since amassed the support of around 80,000 people.