You don't need to have beaten the story to unlock this - Superman unlocks as a playable character after story chapter 7, so just use him to defeat Zod when you fight him for the first time.
You can find Zod by activating the remote computer terminal by the Metro station in the south-east of the map. He appears on top of a building a short distance from the terminal.
It's worth noting that Zod is invincible to most characters so you need to fight him as Superman anyway, irrespective of whether you're after the achievement, in order to beat him and unlock him to be bought.