The former prison officer said she was "over the moon" to land the coveted chart position, just a week after she pipped teenager Nicholas McDonald to the post to win the ITV show.
"Wow wow wow thankyou for getting me to number 1 xx I am over the moon.. Merry Christmas to you all xxx," she tweeted.
Sam, 36, shifted 149,000 copies of her empowering ballad, making it one of the fastest selling singles of the year and denying Pharrell's 'Happy' the top spot.
As revealed on X Factor, all proceeds from the track will go to Great Ormond Street Hospital Children's Charity and Together For Short Lives, with Chancellor George Osborne previously saying he'd waive VAT.
'Skyscraper' was originally released in 2011 by American singer Demi Lovato, who recorded the song while going through personal issues including drug and alcohol abuse.
Afterwards, Demi said she viewed the song as a cry for help.
Demi had massive success with the track - it shot to the top of the iTunes charts in the US within an hour of its release - and has said she's now pleased to see Sam following in her footsteps.
She tweeted on 17 December: "Congratulations @SamBaileyREAL on winning X Factor UK!! Love your version of Skyscraper!"
Watch Sam performing 'Skyscraper' below:
The X Factor 2013 finale in pictures: Katy Perry, One Direction and more -
Copyright: Rex Features Tom Dymond / Thames