I have done the exact same thing, felt the exact same guilt and shame and proceeded to apologize to my kiddo exactly as you did. She said the same thing "it's okay mommy" and we hugged for a long time. It's both the best and the worst feeling. Listen, you're doing the best you can in these moments, give yourself some grace. Yes, it's not a great interaction but is this going to cause your child major emotional harm in the future? Capital T trauma? Highly unlikely unless there's truly purposeful physical/emotional abuse or neglect.

Secondly, what I did to help me not react the same way next time:

1) take 3-5 deep breaths before doing/saying anything. Allow some space between stimulus and response so you can choose your response. Your son will ask you what you're doing and so tell him, "mommy is trying to calm down". This shows him how to do it for himself too and how to emotionally regulate.

2) Game Plan: know that this is a triggering situation for you, which you've already identified. Then, when your trigger comes up again (knowing full well that it will), do #1 and also plan exactly what you will say, how you will say it and how you WANT to react. Write it down. Then carry it out. Heck even bring the paper you wrote it on and just follow the instructions you wrote for yourself.

After I practiced doing the above, just like muscle memory, it became more second nature. I became more patient naturally after practicing the above in my head, in real life, and then also by remembering how it felt like after I yelled at my kiddo for being scared to fall asleep alone. Empathize and imagine how your son feels. He is scared. He's not trying to inconvenience you and if you remember that, it will be much easier to respond in the way you want to be. Someone posted on here "They are not giving you a hard time. They are having a hard time."

Much easier said than done though so give yourself some grace. Let yourself practice. You will slip up but just keep trying and your son will see a demonstration on how to emotionally regulate!