Autry, who has a team-high six sacks and seven quarterback hits, will miss Sunday's game against the Green Bay Packers.
A player who tests positive for COVID-19 can't return to the team until at least 10 days after the start of symptoms, plus at least 24 hours after symptoms have passed, according to league rules.
Special-teams coordinator Bubba Ventrone will also miss Sunday's game for coronavirus-related issues. Colts coach Frank Reich said assistant special-teams coach Frank Ross will lead the unit against the Packers.
The good news for the Colts, though, is that fellow defensive linemen Grover Stewart, Tyquan Lewis and Al-Quadin Muhammad, who were all held out of practice for precautionary reasons Thursday, practiced Friday after it was determined they weren't high-risk close contacts.