The record label executive was due to judge wannabes in Manchester, north-west England alongside fellow panellists Alesha Dixon, Amanda Holden and David Walliams, but he skipped the session when he began experiencing a severe headache.
Walliams joked to the audience: "I wasn't feeling well yesterday and he kept saying, 'Don't come near me' - but I couldn't help myself."
Holden added: "It's ace when he isn't here. We can have our say and relax and drink lots of champagne at his expense."
The Sun newspaper reported Cowell returned to the panel at 8pm.