The PlayStation 2 and PlayStation Portable versions were released as Spider-Man: Web of Shadows – Amazing Allies Edition and are drastically different from the console and PC version. These versions do not feature an open world, and are instead 2.5D side-scrolling brawlers. Players can alternate between Spider-Man's two costumes at any time during gameplay, with the game providing several scenarios in which one suit is more useful than the other. For example, there are several weak walls which can only be destroyed by the black suited Spider-Man. Each suit has individual upgrades, which unlock new combos or increase Spider-Man's health bar.
Like its title suggests, this version puts more emphasis on the ally system than the other versions, providing the biggest variety of allies and consumable power-ups. Instead of cutscenes, the game features dialogue trees, during which the player must select Spider-Man's replies from several different options, which can make Spider-Man appear respectful, mean, or neutral. Depending on which reply is chosen, the player will receive upgrade points for Spider-Man's red suit, black suit, or both. These sections function similarly to the moral choices in the console and PC version, and can have a major impact on the game's story.