"While it's difficult news to receive, as I really looked forward to playing this week, my focus now is on recovery for the final stretch of the fall," Scott said in a statement.
He will self-isolate in accordance with CDC guidelines, and first alternate Jim Herman will replace him in the tournament, which begins Thursday.
Scott last played at the U.S. Open in September. The 40-year-old Australian said in May he was surprised the Tour's testing plan wasn't tighter.
More than a handful of PGA golfers have tested positive, including world No. 1 Dustin Johnson, who pulled out of the CJ Cup last week.