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It's the second year in a row the Hamilton-born, Melbourne-based star has won the top female award.
The 22-year-old was presented the award by British comedian Russell Brand.
The award tops a massive year for the star, led by the popularity of her duet with Australian artist Gotye on world-wide No 1 hit Somebody That I Used To Know.
At last night's awards Kimbra said the ARIA award was an amazing way to top off a "whirlwind" year.
"I want to thank all the fans out there that came to see me play back in those days."
After the awards Kimbra tweeted: "Such a fun & fantastic night at the #ARIAS2012 tonight x thankyou! So stoked to have won Best Female Artist 2 years in a row! Wow!"
Early this month Kimbra scored five wins at the Vodafone New Zealand Music Awards including album of the year and best female solo artist.
Last month Kimbra told APNZ she was planning to take things a bit slower next year, but admitted she was looking forward to a new album.
"The next focus for me is getting into new material. I'm busting to start new songs and I think more than anything I want to find that stability again. I just want to find that stillness where the music comes from.
"I'll be working on [an album] early next year and looking to put something out as soon as it feels ready."