The 24-year-old is the PGA Tour's first positive test in six weeks.
"We are sorry to lose a member of the USGA family in this year's field," the USGA's John Bodenhamer said. "We look forward to welcoming him back to the U.S. Open for many years to come."
Scheffler, who is a nominee for the 2019-20 PGA Tour Rookie of the Year, was in great form leading into the week at Winged Foot. He shot the second-lowest 72-hole score at the Tour Championship and had two other top-five results in his last four starts, including a T-4 showing at the PGA Championship.
Scheffler will be replaced in the 144-man field by South Africa's Branden Grace.
The U.S. Open starts Thursday.