Honda is moving from CSKA Moscow on a free transfer.
"He wanted the No 10 shirt and we made him happy," said Milan chief Adriano Galliani.
"He's an excellent player who has always done well up to now. He is presently in Japan, but he will join up with us on December 30.
"He has signed a three-and-a-half-year contract which will expire in June 2017."
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