He tested positive on Tuesday.
The new ban affected some 90,000 troops.
He is also putting the Pentagon and its grounds on "Health Protection Condition C."
The individual was being treated at a local hospital.
Engineers have been working to address some of these problems for the last five years.
Defense Secretary Mark Esper is pledging to improve the way troops are treated while in coronavirus quarantine.
President Donald Trump said he might extend hospital capacity with tent facilities to deal with COVID-19 pandemic.
The Washington Metropolitan Area Transit Authority says the stabbing occurred on the Pentagon station's lower platform.
The number of total visitors to the Pentagon is being drastically reduced, officials said.
"Over the years, we have stacked up crisis response forces and ... we never actually use them," Esper said.