Reps for the actor declared the rumour to be "entirely false" according to Entertainment Weekly.
It had been claimed that the Looper star had been lined up to play the Caped Crusader following his supporting role in The Dark Knight Rises.
Gordon-Levitt previously told Digital Spy that he liked the fact that Christopher Nolan's franchise offered a complete and enclosed trilogy with "a very satisfying end".
Man of Steel director Zack Snyder recently teased that his Superman reboot may tie into Justice League.
Gangster Squad screenwriter Will Beall is working on Warner Bros' Justice League script. A director is yet to be confirmed.
Photo gallery - The Dark Knight Rises in pictures: