The tennis player called the umpire a "thief" and claimed she was being treated differently to how men would be in the same context.
And the cartoonist, Mark Knight, said he had "no knowledge of those cartoons or that [Jim Crow] period".
For its Wednesday edition, the Herald Sun filled its front page with cartoons, including the contentious Williams image, along with likenesses of USA president Donald Trump, North Korean leader Kim Jong Un and Australian prime minister Scott Morrison.
The newspaper also posted a news story on the reaction to the cartoon, arguing that it was mostly people outside of Australia who disapproved of it.
The original cartoon depicts Williams stomping on her tennis racket, with a pacifier nearby, and the umpire asking her opponent, Naomi Osaka, "Can you just let her win?"
The incident has split the tennis community.
It is well known that Williams is one of Osaka's idols but she's now opened up on how she narrowly avoided bumping into another of her heroes at the US Open.
After the match, Williams would declare, "I'm here fighting for women's rights and for women's equality and for all kinds of stuff".More news: Brexit talks "closing in on workable solutions", Raab says
"This despicable cartoon tried and failed to diminish the greatness & grace of @serenawilliams".
Some also said Knight had "whitewashed" Osaka, whose father is Haitian and mother Japanese.
The Herald Sun reported on Tuesday that Knight had been mentioned on Twitter almost 74,000 times following the cartoon's publication.
"The PC brigade are way off the mark. again", the director wrote on Twitter.
Australian newspaper Herald Sun reprinted a controversial illustration of Serena Williams after her argument at the US Open.
"I don't cheat", Williams told the umpire chair, Carlos Ramos, as he gave her the first violation when she received coaching during the match. He did what he had to do in that match because she overstepped the limit. He portrayed Williams with exaggerated features like oversized lips, a big nose, and wiry hair.
Popular author JK Rowling said on Twitter, "Well done on reducing one of the greatest sportswomen alive to racist and sexist tropes and turning a second great sportswoman into a faceless prop". Lynne Adams tweeted on Tuesday, "Serena Williams is a large black woman who had a complete meltdown, what is racist about this cartoon". "There's a lot of men out here that have said a lot of things, and because they are men, that doesn't happen to them", Williams said to the umpire, Fox News reported.