And staff at the universities, hospitals, and affiliated institutions - which numbers in the thousands - could face layoffs as programs are reconfigured.
"Let there be no doubt about it, this change is going to happen," Christie said at a news conference in Trenton. "I'm going to put the full force of the governor's office behind these recommendations."
UMDNJ would cease to exist in name; University Hospital in Newark, the osteopathic school in Stratford, and other institutions would operate under the banner of a New Jersey Health Sciences University, to be based in Newark.
The school, plagued by scandal over the last decade, would lose the Robert Wood Johnson School of Medicine, the School of Public Health, and the Cancer Institute of New Jersey to the Rutgers system.
Christie painted the mergers as a means to improve a mediocre state university system that has failed to attract research dollars to the degree of other institutions.
"Rutgers is good but not great, and we can't compete with good and not great," he said.
Led by Democratic leader and Cooper chairman George E. Norcross III, South Jersey political and business leaders have pushed for a southern research university as a means to grow regional industry.
"This is a once-in-a-generation thing," said Cooper chief executive officer John Sheridan. "This part of the state has been underfunded for years in terms of higher education."
In Glassboro, news that Rowan's student body could soon grow from around 11,000 to almost 17,000 stirred the imaginations of university officials.
"It will enable us to do the many, many things we couldn't do before: graduate professional degree programs like medicine, public health, biomedical engineering," interim President Ali A. Houshmand said. "It's an exciting time."