Since the OP specified that characters known by an alias count, one of the most prominent examples is probably Revan.
This alias was bestowed on him early in his life as a Jedi Knight when he led an unauthorized expedition to fight the Mandalorians, who were invading systems near Republic space. The Republic media dubbed him "the Revanchist" (I'm not sure that's completely accurate, politically speaking, but never mind), which he later shortened to just "Revan". Under this name he led the Republic to victory in the Mandalorian Wars, then sided with the Sith and invaded the Republic, then had some later adventures which are frankly very bizarre, which I won't try to summarize here.
In his early appearances in the Knights of the Old Republic comics, before taking up his alias, great pains are taken to avoid giving him a name or appearance, identifying him only as a young Jedi Knight and a friend of another promising Jedi named Alek.
In all of his other appearances, including both Knights of the Old Republic games (which take place after his defeat by the Republic but heavily feature him as a background character), his namesake book (where he is, naturally, a viewpoint character), and The Old Republic (where he is a recurring NPC in a number of plot arcs, including his own namesake expansion), he is simply known as "Revan".
Even in the first Knights of the Old Republic game, where the player character is Revan under a false identity, no hint of his true name is given. Although the player can enter any name they want at the beginning of the game, this is the name of the false ID, not of Revan himself. This is in contrast to the player character of Knights of the Old Republic II, who eventually had a canonical name given.