Brown, whose conspiracy thriller has sold more than 17 million copies around the world and has been translated into 44 languages, was not in Britain to accept the prize. Instead he delivered a videotaped acceptance speech, played Wednesday at the British Book Awards ceremony in London.
"For the record, it is a novel," Brown said of his book, which has ignited a religious debate around the world.
Allegations in the novel that Jesus Christ married Mary Magdalene and has descendants have outraged many Christians and have been dismissed by historians and theologians. Among the more outspoken critics was Cardinal Tarcisio Bertone, a former Vatican official, who has said that "The Da Vinci Code" espoused heresy.
Other winners at Wednesday's awards ceremony included former president Bill Clinton whose autobiography, "My Life," won biography of the year.
British actress Sheila Hancock was named author of the year, for her book, "The Two of Us: My Life With John Thaw," a frank account of her marriage to the late Thaw, also an actor.