The image, published on Wednesday in the Columbia Daily Tribune, was flagged by media reporter Jim Romenesko after considerable backlash over social media.
The cartoon by Gary McCoy depicted blacks in Ferguson marching with protest signs displaying messages such as "Burn Ferguson," "Steal to Honor Michael," and "No 60-inch Plasma TV, No Peace!"
The paper's managing editor Jim Robertson told Romenesko the cartoon was only criticizing the presence of looters amid peaceful protests against the police killing of unarmed teenager Michael Brown.
"Provocative yes," he said. "Racist? Certainly not in intent."
Correction: This post has been updated to show that the cartoon never appeared on the newspaper's website.