"The fight was animated, but the incident is over. The two players cleared up their disagreement," Milan chief executive Adriano Galliani was quoted as saying on the italian club's website.
"I'm happy when I see players pumped up, I'm happier seeing fiery training sessions than boring ones."
Reports said Sweden's occasionally combustible Ibrahimovic, an August signing from Barcelona, rashly tackled United States defender Onyewu from behind.
The American, who missed a year of action with a knee injury and has not featured for Milan this term, reacted angrily and the duo grappled before being pulled apart.
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