On her show, she described the 45-year-old actor - who has recently been nominated for an Oscar for his performance in Joker - as 'oddly attractive' before moving on to his 'hairline fracture'.
She said: "He's got one of those, what do you call it? Cleft lip, cleft palate."
Holding up her top lip with her finger, she added: "I find it to be very attractive."
But while she may find Phoenix to be very attractive, lots of people found her mimicking to be pretty disgusting. Canadian American football player Adam Bighill - who was born with a cleft lip and whose son, Beau, was also born with one too - was among those to condemn Williams, describing her behaviour as 'hideous and offensive'.
A cleft and palate is a facial birth defect which occurs when parts of the face do not join together properly during development in the womb and it can lead to feeding, hearing, dental and speech problems.
Williams has now apologised for her remarks - almost 10 days later - and said her show would be donating to cleft palate charities.
Bighill has since accepted Williams' belated apology.
In a tweet, he said: "Thank you @WendyWilliams for your apology, your donation, and for thinking of Beau today for his surgery. I forgive you, and I encourage others to as well. I wish you all the best."Featured Image Credit: YouTube/The Wendy Williams Show