The game promts you through this pretty well. When told to, enter cover at the corner. Watch Zsasz (I don't recommend detective vision here). When he stick his head out, hit him with the Batarang. Walk over and subdue him.
If Zsasz sees you, you will fail. I'm also told that if you wait too long Joker will convince him to kill her anyway. Some have recommended the remote-control batarang, but I found it clumsy compared to a targeted normal one.