The Rossoneri were comprehensively out-played at the Stadio Manuzzi with Zlatan Ibrahimovic missing a late penalty.
Alexandre Pato had two goals ruled out - one for offside, another for a handling offence - while the flag was often raised incorrectly.
"I said 'Forza Milan' yesterday, but it went badly. Never mind, these things happen in football," said Berlusconi.
"Milan were unlucky, even if I think the referee disallowed three good goals."