The song won the prize for Best Original Music and Lyrics for the program Saturday Night Live at the 59th Creative Arts Emmy Awards last night (September 8) in Los Angeles.
Timberlake teamed up with comic Andy Samberg to make the song, which spoofed early-'90s R&B/pop acts like Color Me Badd.
Samberg told the audience : "Justin, if you're out there, congrats to you, kid."
The video beat two songs from a musical version of Scrubs to win the award.
Samberg said : "I think it's safe to say that when we first set out to make this song, we were all thinking, 'Emmy!'
"The other thing we were thinking was, 'Hey! There's this young up-and-comer, Justin Timberlake, who is clearly very talented and could really use a break."
Although Timberlake was not present at the ceremony Samberg said he would be willing to perform the song with the singer at the main Primetime Emmys ceremony, to be held in Los Angeles on September 16, reports the BBC.
For more on Justin Timberlake, check out his NME.com page.
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