The awards, which acknowledge comic books and their creators, were held yesterday at London's MCM Expo.
DWM fought off competition from 2000 AD, CLiNT Magazine, Judge Dredd the Megazine and STRIP Magazine.
The magazine's official Twitter account thanked voters and posted a picture of the trophy (above).
@DWMtweets: We're delighted to announce that Doctor Who Magazine has won the Eagle Award for 'Best British Comicbook Colour'. Thanks so much for voting!
Steven Moffat congratulated the win: "Punching the air
@TomSpilsbury and team with an Eagle Award for Doctor Who Magazine! AMAZING!"
Doctor Who Magazine editor Tom Spilsbury expressed his excitement on winning, posting: "OH MY GOD, WE WON!!!"