The track, which has been in the charts for seven weeks, climbed up from number three to claim the top spot.
GaGa, who performed on last week's X Factor, already has the UK's biggest-selling single of the year so far with 'Poker Face' and currently holds the title for the biggest-selling album of 2009 with The Fame.
The only new entry in the singles chart is Chuckie and LMFAO's 'Let The Bass Kick In Miami Girl', which reached number nine.
Chipmunk climbed up nine places to number ten with 'Look For Me', while Timbaland moved up to number six with 'Morning After Dark'.
Elsewhere in the chart, the X Factor Finalists dropped out of the top ten with 'You Are Not Alone', sliding six places to number 11.
The top ten singles in full (click for our reviews):
1. (3) Lady GaGa: 'Bad Romance'
2. (1) Peter Kay's Animated All Star Band: 'The Official BBC Children In Need Medley'
3. (2) Rihanna: 'Russian Roulette'
4. (4) Black Eyed Peas: 'Meet Me Halfway'
5. (7) Ke$ha: 'Tik Tok'
6. (9) Timbaland ft. Nelly Furtado, SoShy: 'Morning After Dark'
7. (6) Jason Derulo: 'Whatcha Say'
8. (8) Alicia Keys: 'Doesn't Mean Anything'
9. (-) Chuckie and LMFAO: 'Let The Bass Kick In Miami Girl'
10. (19) Chipmunk ft. Talay Riley: 'Look For Me'
Source: Official Charts Company
> Click here for this week's top ten albums