It's possible you are thinking of:
* "The Savage Time" (Justice League Unlimited, 2004-2006): In this episode, Superman is temporarily killed by the time-traveling villain, Chronos. However, he is later resurrected by the Time Trapper.
* "The Doomsday Sanction" (Justice League Unlimited, 2004-2006): This episode features the iconic "Death of Superman" storyline. However, Superman is ultimately resurrected after a lengthy battle with Doomsday.
There is no episode of the *Justice League* animated series where Superman dies permanently.