Wadi-a-Hussain (a.s.) (Wadi-e-Hussain to type it correctly), is the only online graveyard of Karachi. They don't have an interactive services to book a grave, but they do have their contact number (Contact name: Syed Mohd Alam Zaidi Number:92-021-6360079) through which you can ask how to get a grave booked.
The method is simple, you go to Imambargah Khairul Amal, pay them a sum of 7000 Rs., and get a receipt which confirms a grave booked. They make the title slab on their own, so you don't need to order it separately (this is as per my conversation with the representative I called).
My friend asked to get a grave for the burial of her wife's belongings. I will go there on friday to help him out with this...