There are different versions, but "et tu, Brute?" wasn't one. That's probably Shakespeare's adaption of Suetonius' "kai su, teknon?" "You too, child?" This is an attractive option because Caesar seemed to like saying things in Greek at important moments (for instance, the words Caesar is famously supposed to say when crossing the Rubicon, "iacta alea est" seems to be a Latin rendering of the Greek phrase "anerriphtho kybos" - and the language matters; the Latin says "the die have been cast" while the Greek says - forgive my loose translation "let'm roll" - so the potential of the situation is entirely different. In Latin, the roll of the dice is already decided and all that remains is to play out the game, while in Greek we're just now throwing the dice and we don't know whether we'll get seven or snake eyes).

Plutarch, writing in Greek, says when Casca stabbed Caesar, Caesar said in Latin "miarotate Kaska, ti poieis?" (again, loose translation) "Casca, you bastard, what are you doing?" and was silent after that.

Appian doesn't report any last words.

The honest answer would be that we simply do not know, and likely he didn't speak during his assassination. There are no accounts of his death written by contemporary witnesses; those closest in time are from Plutarch and Sueton.

The last words Plutarch lets Caesar utter are "Accursed Casca, what does thou?", when hit by first dagger, and otherwise did not speak at all during the accounter. These words are missing from Suetonius, here Caesar cries "Why this violence?" when his Toga is grasped by one of the conspirators, but likewise does not speak anymore once the attack begins.

However, Sueton remarks that:

in this wise he was stabbed with three and twenty wounds, uttering not a word, but merely a groan at the first stroke, though some have written that when Marcus Brutus rushed at him, he said in Greek, "You too, my child?"

In that case his last words would have been "κὰι σύ, τέκνον;"; kai su, teknon?

Now, the historic Caesar by all probability died in silence, maybe a few grunts or screams. The apocryphal "kai su, teknon?" however took on a life of all its own. It's more an expression of disappointment in Brutus' participation, not an acknowledgement of fathership as some have suggested. It's possible that it also had apotropaic function, on inscriptions there is often a "kai su" or "et tu" in a warding function, and on epitaphs it is often employed to say "it will get you too", "you'll get yours". So it's probable that Suetons anonymous sources thought these would be proper last words, maybe a curse, for Caesar to lay in his mouth, and its popularity has ensured that the phrase took on a life of its own - I've never seen the "Et tu, Brute, contra me?" you quoted, but it nicely conveys the disappointment Caesar might have felt. Thus we also get the popular "Et tu, Brute?" in Shakespeare through various older pieces. As the Italians say, se non è vero, è ben trovato - if it's not true, it is well invented.