According to BBC, the book follows the experience of Matthew Holmes, a 19-year-old who is haunted after witnessing his brother's death at a holiday park in Dorset.
Chairman of the judges author Rose Tremain said it was "astonishingly sure-footed" for a first novel.
"It is not just about schizophrenia - it is about grief," she said.
Filer, a former mental health nurse, looked shocked as he picked up his £30,000 prize at a ceremony in central London.
He said he hadn't prepared a speech as he had checked the betting odds earlier. He thanked the judges and his wife Emily, whom he married last week.
Filer beat best-selling novelist Kate Atkinson, whose 'Life After Life' - a tale of perpetual resurrection - was the bookmakers' favourite to win the overall prize.
Also in the running were Lucy Hughes-Hallett for 'The Pike,' an account of the life of Italian poet Gabriele D'Annunzio, and poet Michael Symmons Roberts for his sixth collection 'Drysalter.'
The shortlist was completed by Chris Riddell, for his children's book 'Goth Girl And The Ghost Of A Mouse.'
Tremain said there had been "no blood" during the final judging process but added that the decision was "not quite unanimous".
"This book stood out in a very good list. The voice in which the author has chosen to tell his story is perfectly aligned with the subject matter and very well sustained to the end.
"The book is exceptionally moving without being sentimental - we're very much hoping there will be more from this writer."
She added: "To have taken such a marvellously articulated thing from his professional life and to have brought it to life in the way that he has was a fantastic achievement."
'The Shock of the Fall' was snapped up by HarperCollins for a "substantial" six-figure sum.
Jo Brand - another former mental health nurse - has called the story, in which Matthew is "managed" by his local community health team, "one of the best books about mental illness".
'The Shock of the Fall' is the fifth first novel to take the overall prize. Kate Atkinson won for her debut novel, 'Behind the Scenes at the Museum,' in 1995.
'The Tenderness of Wolves' by Stef Penney was the last first novel to win the overall award in 2006.
Since the introduction of the Book of the Year award in 1985, it has been won eleven times by a novel, five times by a first novel, five times by a biography, five times by a collection of poetry and once by a children's book.
The Costa Book Awards, formerly known as the Whitbread, is open to authors resident in the UK and Ireland. All five shortlisted authors receive £5,000 with the overall winner getting a further £30,000.
Last year's top prize went to 'Bring Up the Bodies' by Hilary Mantel. It was the first book to be named as Costa book of the year and win the Man Booker Prize in the same year.
Tuesday's ceremony also saw the announcement of the winner of the Costa Short Story Award.
Writer and poet Angela Readman, from Newcastle, won the public vote to win £3,500 for her story, 'The Keeper of the Jackalopes.'