The encounter was abandoned midway through the first half when Rossoneri players decided to leave the pitch, after the 25-year-old kicked the ball toward the home supporters' stands after receiving abuse.
"We are disappointed and saddened by what has happened,” the 45-year-old told reporters after the match. "Milan play for the right to respect all players. We need to stop these uncivilized gestures. We are sorry for all the other fans who came here for a beautiful day of sport.
"We promise to return, and we are sorry for the club and players of Pro Patria, but we could not make any other decision. I hope it can be an important signal."
Manchester City captain Vincent Kompany also commented on the incident, and called for stricter punishment for the offenders.
"Act of racism against Boateng during Milan's friendly. How about becoming extremely intolerant towards racist idiots? They need to be told," the 26-year-old wrote on Twitter.
"I can only salute Milan's decision to leave the pitch. Also noted that the majority of the fans were completely supportive of the players," he concluded.