Fowlkes, 47, followed Holmes, 46, to the home of a detective he suspected she was seeing romantically, the paper reported.
He allegedly began pummeling her on the front lawn. A friend heard Holmes' screams and chased Fowlkes away.
Suffolk County police arrested Fowlkes Tuesday on charges of misdemeanor assault, trespassing and criminal mischief. Fowlkes was released after arraignment and is scheduled to return to court April 8.
A judge granted Holmes, the commander of the 81st Precinct in Bedford-Stuyvesant in Brooklyn, an order of protection against Fowlkes.
The couple had been separated and living in different apartments, officials familiar with the investigation told the News.