The Japanese midfielder also set up the first goal in the fifth minute as Milan ended an embarrassing run of three successive defeats against the Griffins.
Milan, who have failed to qualify for Europe in the last two seasons, stayed sixth in Serie A with 43 points, four adrift of third-placed Roma, who are in the Champions League playoff spot.
Having already forced a superb early save from Mattia Perin, Honda chased a long ball to the byline, just kept it in play and crossed to the far post where Carlos Bacca fired home, the Colombian's 13th league goal of the season.
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A disappointingly small crowd braved the dank conditions for the lunchtime kickoff but they were rewarded when Honda unleashed a 30-metre strike which bounced awkwardly just in front of Perin and flew into the net in the 64th minute.
It was his first goal since he scored against Verona in October 2014.
There was more for Milan to cheer when French striker Jeremy Menez came on for his first appearance following an eight-month injury layoff.
Milan were given a scare when Alessio Cerci pulled a goal back in stoppage time, bundling the ball over the line after 16-year-old goalkeeper Gianluigi Donnarumma parried Tim Matavz's shot.
(Writing by Brian Homewood; editing by Toby Davis)
