For pizza in Prahran I'd recommend Ladro on Greville St. The base is really thin with crunchy crust and there's a great amount of topping options that you can customise with optional extras. There's also one on Gertrude St in Fitzroy http://ladro.com.au/.
I also like the wood-fired pizzas at the Pizza Gallery just a short drive from Prahran on Malvern Road. They have the biggest dine-in pizza menu I've ever seen with inventive topping options. https://thepizzagallery.net/