There is an area of Menteng behind Sudirman that has a large number of shops selling fish, supplies and equipment. While they do have a lot of salt water stuff, you can certainly set up and stock a fresh-water tank. We have a tank full of discus and everything is from that area (except for a few supplies bought at Ace Hardware).
There are also pet stores on practically every corner of Kemang, for reasons I don't quite get. Simple supplies like fish food are usually available there, although I would go to the pasar for any significant purchases, as you are likely to get a better price.