If your destination is Messina or even Catania, you can can save some time leaving the train in Villa San Giovanni (last stop before the train will be loaded into the ferry) and, literally, jump on the first ferry that is starting, so you save all the time needed to load and unload the train.
No one will ask you for a ticket (no one will ask for anything, actually). Or at the least it was like this some twenty years ago when I did it.
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This is also a great way to randomly arrive in Siracusa wondering how did you end up there, in some sort of re-enactment of the last Indiana Jones movie.
Well, I guess I was lucky! More seriously: I just followed a local that suggested this, and he knew the right way but from what I remember, it wasn't that hard to catch the right ferry. And, honestly, after so many hours of train, I was happy to physically move around and not wait another 40+ minutes.