You can get a can of spray-foam, about $6 at HD or most hardware stores. It is essentially a one-shot item because the material in the dispenser stem cures and plugs up, so if you have a lot of places to seal you can do them all at once.
The foam is easy to remove when you need to service it.
You could also use roof mastic, filling the space in multiple applications. One gallon will leave a lot left over for fixing your roof.
If it is not a big hole you can get tubes of caulking compound. I recently used some "driveway crack caulking" which is probably close to the black stuff you chipped out.