Charities will receive the VAT from the sales of the X Factor winner's single for the sixth year running.
It means children's charities Together for Short Lives and Shooting Star Chase will receive 100% of the profits from each download.
Chancellor Philip Hammond praised their "fantastic" work supporting children with life-limiting illnesses.
The government has waived VAT for a number of charity songs, including the Band Aid Ebola single.
The 2011's Military Wives Choir single and the 2010 Haiti earthquake appeal single were also given the exemption.
The X Factor song is yet to be announced but will be downloadable after the winner has been named during the live final on Sunday 11 December.
The chancellor said: "I'm delighted to be able to help by handing back the VAT on sales of the single to ensure that as much money as possible goes to supporting these fantastic charities."
Barbara Gelb, CEO of Together for Short Lives, said it was an "amazing early Christmas present" for the children and young people it works with.
"Working with the X Factor over many years has been transformational, not least in raising awareness of children's and families' needs and giving them much needed voice and support."
David Burland, chief executive of Shooting Star Chase, said he was delighted to be receiving a donation.
"Fundraising in today's economic climate is proving increasingly difficult, so we are extremely grateful," he added.
"Their support is a lovely Christmas present to us, and I would encourage everyone to buy the winner's single and help give sick children, and their families, a Christmas to remember."