Austin is one of the most senior members of President Joe Biden's administration to contract the disease.
In a statement, he said he last met Biden on Dec. 21, more than a week before he began experiencing symptoms.
Austin, who is fully vaccinated and has received a booster, said he would retain all authorities whilst he quarantines at home for five days.
He said: "As my doctor made clear to me, my fully vaccinated status -- and the booster I received in early October -- have rendered the infection much more mild than it would otherwise have been".
Last week the Pentagon tightened restrictions at its headquarters over concern about the highly transmissible Omicron variant.
The military is faced with the challenge of maintaining military readiness for troops, often in close quarters on ships and planes.
Roughly 98% of active-duty troops have received the COVID-19 vaccine, which is now mandatory for them.
U.S. authorities registered nearly 347,000 new coronavirus cases on Saturday, according to a Reuters tally.
