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The Potters had already travelled to United's Carrington training ground before the match was hastily called off.
"Stoke City can confirm that manager Michael O'Neill has tested positive for the Covid-19 virus following the latest round of testing on Monday (June 8)", a statement read released by Stoke.
"O'Neill had tested negative in the previous five rounds of testing. He will now follow the relevant guidance and undergo a period of isolation, whilst continuing to be in regular virtual contact with his coaching staff and players."
O'Neill's assistant Billy McKinlay will take charge of first-team affairs during his absence.
O'Neill is in his first season in charge of the Potters, having taken over in November and helped steer the club towards safety after a dismal start to the campaign under Nathan Jones.
The 50-year-old stepped down from his role as Northern Ireland manager in April due to the shutdown.
