The Japan international, who joined the Rossoneri from CSKA Moscow in January, scored his sideâ€™s second goal of the night in the 56th minute when he ran at the Rossoblu defence before chipping over an advancing Mattia Perin.
The goal succeeded Adel Taarabtâ€™s 20th-minute opener which came in similar circumstances although the Moroccan was able to fire his shot low rather than take the aerial route.
An own-goal from Milan keeper Christian Abbiati with less than 20 minutes remaining gave Genoa hope but in the end, Clarence Seedorfâ€™s men got the job done to record their third league win in a row, to move up to 11th on Italyâ€™s top flight table.
Since arriving at the San Siro, Honda has played 12 times in Serie A whilst also making two Coppa Italia appearances for one goal on debut back on January 15.
For breaking stories and all the great banter like us on Facebook: facebook.com/tribalfootball