The unidentified player experienced symptoms while already under self-quarantine, and he was then tested on Sunday. He's since returned to quarantine.
"We can also report that within the past 48 hours his symptoms have dissipated," the Yankees said. "We will continue to follow all protocols and recommendations established by the local and federal public health experts and Major League Baseball."
A different player in New York's minor-league system became the first confirmed case of the virus in North American professional baseball when they tested positive over the weekend.
Right-handed pitcher Denny Larrondo was reportedly the first player to test positive, according to Dan Martin of the New York Post.
The 17-year-old Cuban pitched in 12 games in the Gulf Coast League last season.
Following the first positive test, the club's minor leaguers were all put in quarantine for two weeks.