Re: What to do in this situation?
It sounds like it may be time to get a little physical with him. By that I do not mean going out of your way to foul. Instead, try using your body after the shot goes up to move him out of the picture. If you make it a game of who can reach the highest, it seems you'll come up short. As such, it may be up to your ability to move the attacking player out of the picture a little bit, at least to open up an opportunity for you to leave the ground first.
That said, one-on-one fastbreak missed shot situations can be weird. I understand it's not always as simple as boxing out since bodies are flying in different directions due to momentum. Sometimes it's just about finding a way to survive.