David Johnson did not enter a plea, the news channel NY1 reported. He was served with a restraining order requiring him to stay away from Sherr-una Booker.
Johnson faces charges that include menacing, criminal mischief, harassment and five misdemeanor assault charges.
Paterson, who became governor after Eliot Spitzer resigned amid a prostitution scandal, called Booker after she first accused Johnson of choking her and ripping her Halloween costume. Booker at that time dropped the charges.
The governor refused to comment on the reopening of the case.
Johnson, who is on unpaid leave from Paterson's staff, was released on his own recognizance. He surrendered Thursday morning at the Bronx District Attorney's Office.
A hearing is scheduled Oct. 14 in Domestic Violence Court.