Watney, 39, retired from the RBC Heritage tournament in Hilton Head, South Carolina the Friday before the second round.
Watney tested negative for the virus when he arrived at the event, but was tested again Friday after he said he had symptoms consistent with the disease, according to the PGA Tour.
He traveled privately for the tournament, which started on Thursday, and was not on the flight charter offered by the PGA tour, the organization said.
“Nick will have the full PGA Tour support throughout his self-isolation and recovery period under CDC guidelines,” the PGA tour said in a statement.
A total of 369 people, including players, caddies and essential staff, were tested for Covid-19 before the tournament began, the PGA Tour, said. All of these tests were negative.
The PGA tour declined to comment further, and asked that news agencies and fans respected Watney for privacy.
CNN Jill Martin contributed to this report.