The online reaction was highly critical.
"It's straight bonkers they let her in," one person wrote. "They better have kicked her out."
Another said: "I see no fan. I see an ignorant, disrespectful, fool. Seriously? Is this not 2016?"
Other comments included "unbelievable", "racist", "terribly insensitive" and "(Australia)'s one of the most racist narrow minded countries, ever".
Williams questioned the motives behind the so-called "blacking-up" trend during Wimbledon last year. People posted online photos of themselves with their faces covered in the dark Australian food spreads Vegemite and Nutella.
Kyrgios tweeted that he had no problem with the gesture, which was seen by some as involving racism.
Tennis Australia said no complaints were received about the latest case of face blacking in the Melbourne tournament, the Daily Mail reported.