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 measured 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.
