The TV show judge was forced to miss most of the day's filmed auditions as he was suffering from a migraine.
He later joined David Walliams, Alesha Dixon and Amanda Holden at 8pm at the Manchester auditions.
Walliams joked that it was his fault that Cowell was ill, telling the audience: "I wasn't feeling well yesterday and he kept saying, 'Don't come near me' - but I couldn't help myself."
Amanda 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."
Simon Cowell is said to have put through The Voice UK singer Bill Downs to the next round of Britain's Got Talent.
He will reportedly film a one-off sketch for Comic Relief involving a pretend wedding to a unknown bride.
Watch Simon Cowell, Ant & Dec and the BGT judges chat to Digital Spy below: