The Argentine scored twice before half-time to put Milan in control in the game.
Giacomo Bonaventura added another for the 18-time top-flight champions, before Sergio Pellissier got a consolation.
Higuain's side currently sit 10th in Serie A, a huge 12 points behind leaders Juventus.
The striker now has four goals in six games in all competitions for his club, three of which have come at the San Siro.
7 October 2018