Berlusconi, the younger brother of club president Silvio, was filmed describing new signing Balotelli as "negretto di famiglia'' - translated as "the family's little n*****'' - at a political meeting in Monza on Sunday.
The footage was published on the website of Italian newspaper La Repubblica and received worldwide attention, especially after Milan midfielder Kevin Prince-Boateng won plaudits from Berlusconi senior for walking off the pitch after being racially abused during a friendly last month.
Milan did not issue an apology for Berlusconi's comments, but posted a picture of the two men shaking hands and smiling at each other on their official website.
A statement simply read: "Today the vice-president of AC Milan, Paolo Berlusconi, had a brief conversation with Mario Balotelli while helping out at Milanello (Milan's training ground).''
Berlusconi himself later elaborated, saying: "I spoke to Balotelli, though in reality there was no need seeing as he is an intelligent lad. He had already understood my phrase was an affectionate one that was turned into a stupid media circus.
"Let us close this story as Mario told me there was no need to say anything else."
Italy international Balotelli joined AC Milan from Manchester City on transfer deadline day last week and scored twice on his debut against Udinese at the weekend.
Meanwhile, Balotelli's colourful start to life back in Italy continued on Thursday as he was involved in an altercation with the police after reportedly parking his Audi RS4 in a disabled parking space outside Milan's Linate airport.
Traffic officials asked the AC Milan striker to move his vehicle, but he hardly helped matters when he moved it to another area outside the airport that was assigned as a 'no waiting' zone.
It then emerged that he was not displaying a valid insurance certificate, as is compulsory under Italian law, although the wardens were happy with his British licence which he is allowed to use in Europe.
AC Milan officials have denied suggestions that their new arrival was handed an on-the-spot fine for his antics, but this will be nothing new to the 22-year-old who was famous for collecting parking fines during his turbulent spell in England with Manchester City.
Information from the Press Association was used in this report