The first big moment of the match came in the 18th minute, when the home side controversially had a goal ruled out.
Stephan El Shaarawy then curled an effort wide from edge of the box, before Bonaventura drilled a shot off target as Milan continued to dominate.
Menez was the next to threaten for the Rossoneri, as he latched onto a loose ball inside the box and fired a strike narrowly wide of the far post.
Keisuke Honda had the final chance of the half for Milan with a low drive from inside the box, but the Japanese international could only direct his attempt straight at the keeper.
In the 62nd minute, Milan were awarded a penalty when Maurizio Domizzi dragged down Honda inside the box.
Domizzi was shown a red card for his challenge and Menez confidently slotted the ball into the corner from the resulting spot kick.
Milan soon found themselves down to 10 men too, as Michael Essien was sent off for picking up his second booking of the match.
The dismissal did not have an adverse effect on the hosts as they quickly scored a second.
Menez drove into the box from the left, before placing a low strike into the bottom corner.