The 27-year-old, who impressed in the U.S. side's run to the Confederations Cup final last month, has joined on a free transfer from Standard Liege and penned a three-year contract.
The club announced the signing on their website and pointed out he holds a Belgian passport, which means Onyewu will not count as one of only two non-EU players Italian sides are allowed to sign each season.
Milan's interest in the defender had barely been mentioned in the media and his signing comes just a day after hundreds of fans protested at the first day of pre-season training.
They are seeking a new striker with Real forward Klaas Jan Huntelaar, Sevilla's Luis Fabiano, Arsenal striker Emmanuel Adebayor and VfL Wolfsburg's Edin Dzeko in the frame.
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