The driver of the car can be heard laughing as it chases after the animal and can be heard saying, "You got him, hit him, hit him, kill him".
The man then hits the wombat in the head twice with a stone, causing it to fall to the ground before he can be seen celebrating to the camera with his arms outstretched.
"You killed him!" the driver can be heard saying. "First bloke I've ever seen kill a wombat on foot, bro."
Police Commissioner Grant Stevens said he had viewed the video found the actions portrayed to be "totally abhorrent and unacceptable."
"I am aware of the community outrage regarding this manner," he said.
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"I want to reassure everybody that the actions in the video do not align with the values and behaviours I expect from my employees, nor does it align with community standards.
"Numerous employees of South Australia Police have also expressed to me that they, too, find the footage detestable and not consistent with their values."
The video has gone viral with hundreds of comments and shares.
The Wombat Awareness Organisation has launched a petition calling for native animals to be protected under the Animal Welfare Act and for the man to be prosecuted.
The petition, which notes that although the act of stoning the wombat to death was allowed under the Native Title Act and accepted as traditional hunting, it contradicted Part 3 Section 3 of the Animal Welfare Act.
"Heartbroken ... this is tragic," the post read.
"I am tired of reporting such cruelty for it to be ignored ... This has to stop!"
The petition had more than 12,000 signatures at 4.30pm AEDT.