Moffat will be recognised for his outstanding creative writing contribution to British television over the last 23 years, which has included work on children's TV, comedy and primetime drama.
"Blimey! A Special Award! I didn't even know I was ill! So thrilled by this - especially after two years of Sherlock and Doctor Who, my two favourite shows ever," said Moffat.
"Of course the work, and the people I get to work with, has always been all the reward I need - a fact I'm very glad that BAFTA has disregarded."
Moffat's TV career began in 1989 on CITV series Press Gang, which helped launch the careers of Julia Sawalha and Dexter Fletcher.
He went on to write for comedy series Murder Most Horrid, Joking Apart, Chalk and most famously Coupling.
Moffat's work on Doctor Who - a show he had been a fan of since childhood - began with a Comic Relief Red Nose Day parody, Doctor Who and the Curse of Fatal Death.
Steven Moffat's greatest work - Picture gallery:
Copyright: PA Images Gareth Fuller/PA Wire
He went on to become one of the most popular writers of the revived BBC One sci-fi series, eventually replacing Russell T Davies as showrunner in 2010.
The 50-year-old Scottish writer was also behind BBC One's Jekyll, the huge ratings hit Sherlock and co-wrote the 2011 big screen adventure The Adventures of Tintin: The Secret of the Unicorn at the request of Steven Spielberg.
Tim Corrie, Chairman of BAFTA, added: "Steven has had an outstanding year with Doctor Who and Sherlock, not to mention the feature film The Adventures of Tintin, and we are delighted to honour his contribution to television and the arts.
"He is one of the finest exponents of his craft and his award, presented in honour of the late, great Dennis Potter, is very well deserved indeed."
Previous recipients of the 'Special Award' include Russell T Davies, Paul Abbott, Alan Plater and Lynda La Plante
The Arqiva British Academy Television Awards will be hosted by Dara O'Briain at the Royal Festival Hall, London, and broadcast on BBC One on Sunday, May 27.