Graphic novels commissioning editor Corinne Pearlman, who judged the prize alongside Rankin, graphic novelists Bryan Talbot, Ed Hillyer and Hannah Berry, and cartoonist Steve Bell, described the winning book as "funny macabre". It will be published by Myriad in 2013.
The Black Project is about a boy, Richard, who begins making girlfriends out of clothes and objects. The book uses illustrations combining embroidery, print making and lino cuts. Pearlman said: "We had an incredible shortlist and we felt all the submissions were extremely publishable.
"We weren't expecting a fait accompli, and we want to work with Gareth to make it into something both he and we are proud of. Working on it together was part of the prize."
Brookes studied Fine Art at the Royal College of Art, but started making small press comics in 2006.