Water – How to seal around this pipe on the roof

If you don't have a problem with water pooling any more, the real answer is probably to have a professional roofer look closely at the roof both on the inside and outside. The problem with a lot of roof leaks is that where the water shows up in the house isn't where it comes in. Water has an annoying tendency to run along internal beams and such, then come into the house far away. You can go over any edges with new tar and hope you catch it but in my experience this approach ends up being like playing whack-a-mole, you patch and wait for it to rain, then patch more and wait more, etc.

So I would say if you can do it yourself, look closely at the underside of the roof as well as the outside. If you don't find anything, a professional roofer is probably in order.

Concrete itself is not waterproof, in fact, it's more like a sponge, so concrete alone is never used to create an impermeable surface. You haven't provided much info - is the roof flat, sloped? What is already up there? There are tons of different waterproofing methods available.

Going under the assumption that it was properly waterproofed at some point, you need to figure out why it's leaking. Maybe there is damage to the roof, or maybe there is a drainage problem and water is just building up and finding its way in. Also possible is that the flashing around a vent or access hole has been bent away and water is getting behind it. Either way, you will first need to investigate and resolve the root problem and then fix it in-line with how it was already constructed. If the roof is tarred, you are not going to put down some other barrier.

You will without a doubt have to go on the roof to check it out. If you're not comfortable with this, its best to call a roofing expert.