Men's magazines dominated this year's awards, with FHM also picking up Best Lifestyle Cover.
GQ's September 2009 cover of actress Sienna Miller was described by judge Jim Bilton, managing director of Wessenden Marketing, as "so good, it looks completely effortless".
The upmarket men's lifestyle magazine also beat contenders Vogue, Harper's Bazaar, Stylist and Look, to fashion cover of the year. GQ editor Dylan Jones said: "I'm thrilled that GQ has won this prestigious award."
Jones added: "Creative director Paul Solomons did a great job. We had a sensational subject, a world class photographer and a smart idea."
Charlotte Zamani, managing editor of GQ, said: "We made [Sienna Miller] one of our best-selling covers of 2009, a year best forgotten by some, maybe, but another memorably successful one for GQ."
, established by online subscription service iSubscribe in 2009, were judged by Media Week editor Harriet Dennys, and CEO of the PPA, Barry McIlheney, among other industry figureheads.
Category winners:
Overall Winner - GQ (September 2009)
Entertainment Winner - Metal Hammer (December 2009)
Fashion Winner - GQ (September 2009)
Lifestyle Winner - FHM (October 2009)
Specialist Winner - New Scientist (5 December 2009)
Sport Winner - Whitelines (January 2009)
Technology Winner - Wired (June 2009)
Trade Winner - Marketing Week (10 December 2009)
Youth Winner - Beano (October 2009)