The mother had intended for her son to look like his idol, AFL player Nic Naitanui, for his school's book week.
But her Facebook post caused a huge outcry from those who saw it as racist.
In a statement, the player said the boy's attempt to emulate his hero "hurts my heart".
The Australian Football League player, who plays for West Coast Eagles, said children were "unaware of the painful significance" of blackface.
Mr Naitanui, who is of Fijian heritage, said on Twitter that he didn't believe the mother had "any intention to cause harm".
But he said she should "reflect and choose an alternate method next time".
"It's a shame racism coexists in an environment where our children should be nurtured not tortured because they are unaware of the painful historical significance blackface has had previously."
The Western Australian mother had originally made her post on the Facebook page of popular blogger Constance Hall.
The woman, who is not being named by the media to protect her child, said her son regarded Mr Naitanui as his idol and he wanted to dress up as him for Book Week.
She said she was worried about "politically correct extremists" but decided to dress him up as he wanted anyway, in an AFL strip, dreadlock wig and with body paint.
"He is pastey white and if I just sent him in a wig and footy gear, no one would tell who he was.
"So I grew a set of balls and painted my boy brown. After being told by everyone not to do it, my son won the parade!"
The post, which has since been deleted, went viral amid widespread debate online.
The mother later posted on her Facebook page that she had been "called every single name under the sun, had my words twisted into other people's negative interpretations".
But she also said she had received messages of support from "amazing women all over the world".
Mrs Hall later said she had also received a backlash, including death threats, for hosting the photo on her page.
In an emotional post, she said she had "never received so much abuse" in her life, and that some was from the woman's family.
"I didn't think I was shaming her at all, I clearly stated that I don't believe she is racist at all, she has a beautiful son with a great hero. I just don't think we should paint our kids in blackface if it offends and hurts people. "
In an earlier post justifying her decision to delete the mother's post, she had said blackface was "hurtful to our indigenous brothers and sisters".
The incident has also sparked furious debate on social media, between people who saw it as racist and people who thought it a child's innocent tribute.
"How is blackface still happening in 2016?" a Twitter user said.
"Dear white people. Please stop trying to defend #Blackface you're making us all look bad," said another.
Briggs, a prominent Indigenous Australian rapper, said on Twitter: "Colour is not a costume."
"All these white dudes telling me I'm 'making it an issue', I hope so. It's your privilege to ignore this stuff - it's my burden call it out."
Briggs also added on his official Facebook page: "It's not the kids fault his mother couldn't pass on better judgement."
"Dressing up as Nic Naitanui isn't blackface," said one person. "The kid wasn't trying to mock Naitanui."
Others also asked how dressing as an AFL player was relevant for Book Week, where children are supposed to dress as their favourite fictional characters.
"Can the 'not' racist mother tell us what Book Nic Nat came from?", another chipped in.
Later on Friday, Naitanui tweeted: "At the end of the day I genuinely admire the kid for looking up to me. Would love to meet the little champion reader."
Earlier this year another AFL player, Adam Goodes, an Indigenous Australian, took time off after he was plagued by booing whilst on the field.
At the time, then Senator Nova Peris - the first Indigenous Australian woman elected to parliament - said the animosity aimed at Goodes was obvious.
"Racism... is alive and well and happening everyday and I know that because I live every day as an Aboriginal person", she said.
An Australian footballer has called for better education about race, after a mother painted her son's skin brown as a tribute to him, drawing widespread criticism.