Is it safe to put fresh hot soup in a glass mason jar?
Since you are asking about canning then what you are describing is not a canning process which will give you a result you can store long term at room temperature. Long-term storage of soup would require pressure canning to raise the internal temperature high enough to kill any foodborne illnesses. 

If you plan to freeze the soup then mason jars aren't ideal, they'll work but they are bulky and take up a lot of room. In any case you don't get any real benefit from putting the lid on when hot if you are going to freeze them, you're better off letting it cool so you don't end up overwhelming your freezer's cooling capacity.