Rage's 'Killing In The Name', which became the subject of a Facebook campaign to stop the X Factor winner getting to number one, was originally given 100/1 odds of making it to the festive top stop two weeks ago.
Bookmaker William Hill later slashed odds to just 3/1 when the race received widespread publicity in the press.
"We discussed never taking bets on Christmas number ones again because X Factor seemed unbeatable," spokesman Rupert Adams said.
"It's hard to say right now how much we've lost. But the industry will definitely be paying out six figures. It could easily be over £1 million."
McElderry later congratulated Rage on their win, calling it an "interesting chart battle".
> Click here for the Christmas singles chart Top 10