It was the perfect start for the hosts as Bonaventura picked out Menez, who burst into the box with a clever touch before slotting past a helpless Rafael Cabral.
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Milan frustrated the visitors with a stubborn defensive display in the first half, and they were unfortunate not to go further ahead when Andrea Poli drilled wide after being released by Keisuke Honda.
However, they were rewarded with a second goal shortly after the break when Pablo Armero's inviting delivery was headed home by Bonaventura.
Napoli struggled to produce a response after falling two goals behind, and Milan looked comfortable defending when the visitors did move forward.