The singer's hit track 'Climax' fought off competition from viral smash 'Gangnam Style' by Psy and Carly Rae Jepsen's 'Call Me Maybe' for the top spot.
Taylor Swift came in at four with her popular single 'We Are Never Ever Getting Back Together', while Nicki Minaj lands at six with 'Roman in Moscow'.
Pussy Riot's 'Putin Lights Up the Fires' - which was released in response to three of their members being found guilty of "hooliganism motivated by religious hatred" for an anti-Vladimir Putin performance - came in seventh place.
Usher's 'Climax' was released back in February and was produced by Diplo. It served as the lead single for his latest album Looking 4 Myself.
TIME magazine's Top 10 'Best Songs of 2012' are as follows:
1. Usher: 'Climax'
2. Psy: 'Gangnam Style'
3. Carly Rae Jepsen: 'Call Me Maybe'
4. Taylor Swift: 'We Are Never Ever Getting Back Together'
5. Parquet Courts: 'Master of My Craft'
6. Skrillex: 'Bangarang'
7. Nicki Minaj: 'Roman in Moscow'
8. Pussy Riot: 'Putin Lights Up the Fires'
9. The Belle Brigade: 'No Time to Think'
10. Can: 'Graublau'
Watch the music video for Usher's 'Climax' below: