Judges praised the News International title and said it stood well above any of its rivals and praised it for its depth of content and features.
"Sun online stands head and shoulders above its rivals and this newspaper shows that you can have a newspaper site with powerful images, and plenty of them, too.
"Judges were not only particularly impressed by the large image sizes, but the surprising depth to the site, offering not just the usual tabloid news and gossip but in-depth special reports laden with pictures, such as their current Falklands and Blair features."
Pete Picton, Sun Online editor, said: "The Sun has always been famous for its pictures. It's great to see that we've continued that tradition online and our ground breaking design has been recognised by fellow journalists."
Other winners at the ceremony, which took place at London's Guildhall, included BBC News, which won News Website of the Year for its large volume of pictures, The Sunday Herald and The Guardian newspapers, which won Newspaper of the Year.
The judges said changing page formats can create particular problems for picture use and even though The Guardian has downsized it "still manages to use pictures with stunning effect".