The group triumphed over tracks such as Little Mix's 'Cannonball', Lou Monte's 'Dominick the Donkey', 'Paradise' by Coldplay and Nirvana's 'Smells Like Teen Spirit' in the race for the festive top spot.
Malone formed the Military Wives Choir - which comprises the wives, partners and girlfriends of serving armed forces members - for his BBC Two factual show The Choir: Military Wives. He offered his congratulations to the choir on Twitter, writing: "Congratulations ladies. You did it. Be very very proud. Gxxxx."
'Wherever You Are' was made VAT exempt following a request from Conservative MP Oliver Colvile, and attracted the largest two-day sales figures for six years earlier this week.
Proceeds from the single will benefit two armed forces charities - the Royal British Legion and SSAFA Forces Help (the Soldiers, Sailors, Airmen and Families Association).
Little Mix drop one place to number two, while Coldplay slide three places to number five.
Lou Monte's 'Dominick the Donkey' enters the Top 40 at number three following a campaign by BBC Radio 1 DJ Chris Moyles. The track shifted nearly 93,000 copies and makes the UK chart for the first time since its original release 51 years ago. YouTube sensation Alex Day sold almost 53,000 copies of his self-released single 'Forever Yours' to take fourth place.
Elsewhere, Olly Murs drops three places to six with 'Dance With Me Tonight', while Rihanna and Calvin Harris slide five to tenth place in the chart. Nirvana's 'Smells Like Teen Spirit' just misses the Top 10 following a Facebook campaign to make it Christmas number one, charting at number 11.
The Top 10 in full:
1. (-) Military Wives Choir and Gareth Malone: 'Wherever You Are'
2. (1) Little Mix: 'Cannonball'
3. (132) Lou Monte: 'Dominick the Donkey'
4. (-) Alex Day: 'Forever Yours'
5. (2) Coldplay: 'Paradise'
6. (3) Olly Murs: 'Dance With Me Tonight'
7. (6) Flo Rida: 'Good Feeling'
8. (4) Lloyd ft. Andre 3000 & Lil Wayne: 'Dedication To My Ex (Miss That)'
9. (7) Avicii: 'Levels'
10. (5) Rihanna ft. Calvin Harris: 'We Found Love'
> This week's albums chart, including the Christmas albums no.1
Source: Official Charts Company