Austin's symptoms were "mild" and he will quarantine at home for the next five days, the Pentagon chief said in a statement, AFP reported.
Austin said he is fully vaccinated and boosted, which had "rendered the infection much more mild than it would otherwise have been."
"The vaccines work and will remain a military medical requirement for our workforce," Austin said. "I continue to encourage everyone eligible for a booster shot to get one."
Austin said he was last in contact with US President Joe Biden on December 21, more than a week before he started to experience symptoms and he tested negative for the virus that morning.
He will retain all authority and attend key meetings and discussions virtually "to the degree possible," he said in the statement.
Austin is the latest high-profile US official to contract COVID-19 as the Omicron variant drives a record surge in infections.
Several prominent members of Congress recently revealed they had tested positive for the virus. Biden's press secretary Jen Psaki contracted COVID-19 in October.