"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.
He'll be replaced in the tournament field by Jim Herman.
Scott won the Genesis Invitational in February but hasn't been in serious contention since he rejoined the Tour in August amid the coronavirus pandemic.
His best finish was a 22nd-place result in the PGA Championship. His most recent start was at the U.S. Open in September, where he finished tied for 38th.
The 40-year-old Australian returned home after the Tour halted play because of the pandemic. He said he considered staying in Australia for the remainder of the year but his outlook changed after the majors were rescheduled for the summer and fall.
"Once the majors were planned to go ahead, I really selfishly could have missed them," Scott told reporters in August. "At the start of this interview, I mentioned how the majors are so important to a player's career, and that's what I'm looking to do now."
The 2013 Masters champion will likely set his sights on returning to action at Augusta on Nov. 12 in pursuit of another Green Jacket.
Scott becomes the 13th golfer to test positive for COVID-19 on the PGA Tour since play resumed.
Play in the Zozo Championship tees off Thursday at Sherwood Country Club in California. Tiger Woods is the defending champion after winning last year's event at Accordia Golf Narashino Country Club in Japan for his record-tying 82nd Tour triumph.