The album was selected from a shortlist that included albums from Radiohead, Bon Iver, Bill Callahan, Fleet Foxes, Josh T Pearson, Paul Simon and Gillian Welch by a panel of judges including BBC Creative head of music entertainment Mark Cooper, comedian Stewart Lee, singer Linda Thompson and Uncut editor Allan Jones.
Jones called the album "a brave and dramatic record", while Cooper described Harvey as "the best British artist of the last 20 years".
There are more details of the award in the current issue of Uncut, while the full transcript of the judging panel's discussions will be published soon on Uncut.co.uk.
In second place for the 2011 prize was Paul Simon's So Beautiful Or So What, while third place went to Gillian Welch's The Harrow And The Harvest.
Harvey told Uncut that she was well into the writing process for her next album.
"I'm quite far into working on what will become my next body of work and again my desire of wanting to learn continues to unfold," she said.
"I began working on my next piece the moment I finished recording Let England Shake over a year ago. I'm well into that next project already".
The previous winners of the award are Fleet Foxes (2008), Tinariwen (2009) and Paul Weller (2010).
Let England Shake has sold almost 100,000 copies in the UK since its release in February, getting a modest boost from its Mercury win in September.
It has also been one of the most critically acclaimed albums of the year and is sure to feature in many end-of-year best of lists.