The Welsh singer let slip “f*** me” as it was announced that his act, Into The Ark, had made it through to the final two of the competition on Sunday night's show.
Sir Tom addressed the incident as he launched the band's first UK headline tour for later this year.
He said: “I was so shocked and because I believe in them so much.
“It gives me a boost to know that the public believe like I do in these boys.”
Host Emma Willis was quick to apologise for Sir Tom's language, saying: “There may have been a little swear word that popped out then through excitement – apologies to anybody if they were offended.”
Into The Ark, made up of Taylor Jones and Dane Lloyd, finished second to Jennifer Hudson's act Mo Adeniran who secured a Polydor recording contract.
Sir Tom wasn’t the only one providing the drama during the final which also saw a stage invasion.
Londoner Dr A.C ran onto the stage as presenter Emma Willis hugged eliminated contestant Jamie Miller.
Security guards were quick to pounce on him before dragging him to the side of the stage as Willis tried to calm the situation.
The Londoner claims he was nearly “choked to death” after being treated like a “criminal” by security and said Willis should apologise to him.
However, a spokesperson for ITV said: “Safety of our audience and cast and crew is of paramount importance, and our security team removed the intruder in a safe and secure manner.”