Authorities say there was a history of prior domestic complaints, and they are investigating whether a restraining order was in place.
The couple had been separated since 2009.
"I want to reassure the residents of Montclair this is a targeted incident," Montclair Police Chief David Sabagh said. "I would also like to commend the Montclair Police and the Homicide Task Force for the swift arrest."
Bail for Khan was set at $1.5 million.
The defendant is originally from Kenya.
In addition to murder, Khan is charged with weapons offenses.