Jones, of Kernersville, North Carolina, turned himself in to police earlier Thursday.
Sandor Szabo died after he tapped on a auto window, mistaking it for his Uber ride, and was allegedly punched by the driver before hitting his head on the pavement in NY.
Szabo later died as a result of his injuries at a NY hospital.
Jones was released on his own recognizance and ordered to return to court October 2. Szabo later died in the hospital after Jones' punch caused him to hit his head on the pavement. He appeared in court in New York City on Thursday and faces a third degree assault charge.
In a statement, Wake Forest said the school would comment further once it gathered more information.
Detectives told ABC New York station WABC-TV that Szabo had just left a family wedding, possibly while intoxicated, and was walking around banging on cars until he then pounded on Jones' SUV.
The investigation is ongoing, and charges against Jones could be upgraded, police said.
Head coach Danny Manning said at the time that Jones was a "well-respected bright mind" in the coaching world and brought "new blood" and "new perspectives" to Wake Forest.
Jones, a Philadelphia native, previously coached at Virginia Commonwealth and Florida Gulf Coast.
His employers described him on Facebook as "super outgoing, friendly, and an incredibly smart businessman".
"He was always upbeat, positive, kind and caring", the post continued. "He was a really good person".