The South London club explained the 28-year-old’s absence soon after Roy Hodgson named his starting XI for the clash at Turf Moor.
They tweeted: “Roy Hodgson has selected Michy Batshuayi for tonight's clash at Burnley, replacing Wilfried Zaha who is omitted from the travelling squad as he is self-isolating.”
Hodgson added: "He has tested positive unfortunately for coronavirus so is self-isolating, and is awaiting the results of the next test.
"He is not feeling particularly ill, but unfortunately the test proved [positive], and he is following the procedures."
Newcastle United face Crystal Palace on Friday night in the Premier League and it is unclear when Zaha will return.