Okay, in Star Wars Insider #88, on pg. 58, it talks about the villians of the Old Republic. Under Darth Malak's paragraph, it says this:
"Malak's most distinguishing feature, his steel jaw, disguises a vicious lightsaber wound inflicted by his former Master in their desperate final battle."
Since Star Wars Insider is always considered canon, Revan did indeed cut Malak's jaw off. Hopefully, well get to see this duel in the K.O.T.O.R comic series. It also states this fact on the back of the box for Darth Malak's action figure.