It is a fungus and it sets in very quickly when the humidity intensifies this time of year. It usually only affects part of the plant and it's best to just cut that limb off and throw it away. Or you can remove the brown liquified areas and it will heal and continue to grow. There's not much that can be done to prevent it. Not what you wanted to hear, but it's just a part of growing dragon fruit here.
Kevin

Thank you for the information! I wish I would have taken care of it when it was affecting a small piece, but I know for what to do in the future. It was indeed very quick, it took about a week to spread throughout this 2 foot section.

I have tried spraying my dragon fruit plants which were infected with black spots with a salt solution of 2-3 tbsp of salt to a gallon of water. My dragon fruit plant are now recovering. It is best to remove the sections badly infected and spray the plants thoroughly with water to clean the entire plant. Do not allow any liquid or infectious matter to drop or scatter over the healthy parts for the same may cause further infection. Spray the plant with the salt solution and allow to dry.