Brilliant mathematician Turing led a team decoding messages at the Bletchley Park base and also designed the "bombe" machine which decrypted German messages.
He was given a post-humous royal pardon in December for his conviction for an act of "gross indecency" in 1952, which led to his chemical castration and the loss of his security clearance for his post-war work. He committed suicide in 1954.
Neil Tennant and Chris Lowe, who first charted as Pet Shop Boys 29 years ago, will perform A Man From The Future, based on Turing's life and work, in full for the first time this summer.
It is one of the 92 concerts of the Proms, announced by outgoing director Roger Wright. Performances will also include the Proms debut of choirmaster Gareth Malone, accompanied by a group of Military Wives.
The Turing premiere will feature in the opening Late Night Prom on July 23 with the BBC Concert Orchestra.
The Pet Shop Boys said: "It is an honour for us to be invited to present some new music at The Proms and to celebrate Alan Turing 60 years after his death."
The work, which will include a narrator, electronic instrumentation and a choir, has its text based on Andrew Hodge's biography, Alan Turing: The Enigma.
The centenary of the start of the First World War will also be marked with a performance of Benjamin Britten's War Requiem and New War Hymn, written by the Proms' founder Sir Henry Wood.