The Sydney-based indie rock band, which is made up of Hayley Mary, Heather Shannon, Nik Kaloper and Sam Lockwood, beat nominated acts such as Gotye, Boy and Bear, Adalita, Jack Ladder, Kimbra, The Middle East, Abbe May and Gurrumul to win the $30,000 cash prize.
According to The ABC, guest speaker David Fricke from Rolling Stone raved about The Jezabels at the awards ceremony, shortly after the music magazine named Prisoner their 'Album of the Year'.
He said: "I got that record as a present from my god-daughter in Adelaide and I immediately loved it and I immediately wrote about it for the magazine in America."
The Jezabels are currently touring overseas, so were unable to attend the ceremony in Sydney on Thursday afternoon.
Earlier this year, there was a public fallout after two of the Australian Music Prize judges accused the nominations list of ignoring niche acts. In response to this, The Jezabels released a statement.
It read: "To all involved in the process of awarding the Australian Music Prize, The Jezabels would like to recognise the difficulty with which you have come to your decisions this year, both in the nominations and the final judging process.
"What is clear throughout all the difference of opinion, regarding both the politics of the prize and musical tastes, is that the AMP is made up of people who care a great deal about Australian music and the importance of maintaining the ideals that the prize has come to represent."
They then thanked the judges and promised that they would put the prize money to good use.
Cloud Control won the Australian Music Prize last year.
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Watch The Jezabels' video for 'Mace Spray' below: