Abayuba Rivas, 39, was ordered held on $2.25 million bail.
Rivas told police his wife left their home to go to the pharmacy last month and never came back.
Investigators believe he killed 32-year-old Karla Jose Villagra Garzon and dumped her body in an empty home in Chatham Township.
She was found about three weeks after she disappeared on February 22.
An intensive joint investigation involving the Elizabeth Police Department, the Union County Homicide Task Force and the New Jersey State Police Missing Persons Unit led to Rivas being identified as the primary suspect in the case.
An autopsy revealed that Garzon's cause of death was asphyxiation, with blunt-force trauma contributing.
