Who is this man changing the name of Little Dice to Li'll Z?

He doesn't appear to have a name. Interestingly, TV Tropes lists this as a meaningful rename trope:

The name is the thing, and the true name is the true thing — so if the name changes...

Some names have obvious meanings but often, this is done when it is not the original name for the person, place or object, but rather, a new one given by someone or assumed.

On City of God they say:

In City of God, Lil Dice gets the new name Lil Ze from a religious practitioner, who states his new name will change his fate.

This is discussed in a 2004 article I found, which includes quotes from an interview with the film's director Fernando Meirelles:

City of God also drapes itself in layers of subplot, resulting in a complex web of detail that can only be fully absorbed through repeated viewings. One surreal scene, for instance, shows Lil’ Ze’s ritual transformation from child to man, as he visits a sinister witch doctor’s candle-lit cathedral. “This amulet is your protector,” the elder explains, placing a necklace around the killer’s neck. Many viewers might easily miss the significance of this witch doctor’s insistence that Lil’ Ze not fornicate while wearing the amulet. Watch City of God a second time, however, it becomes clear that the hood’s violation of this command is the catalyst for his undoing.

“The scene with the witch doctor,” explains Meirelles, “comes from a religion brought to Brazil from Africa, called Candonble, that incorporates a lot of saints and entities, like gods that protect the sea and the winds. Different archetypes called orixas. In this scene, a very mean orixa – presented through the witch doctor - gives Lil’ Ze’ his power. But he is told that he can’t screw anybody with that amulet on. Later he rapes a girl. We don’t see the rape actually happen. Instead, there are three seconds showing only the amulet.”

So the man in the scene is some type of witch doctor although his exact name isn't revealed.